AGIOS PHARMACEUTICALS, INC. Condensed Consolidated Balance Sheets (Unaudited) (In thousands, except share and per share data) June 30, 2026 December 31, 2025 Assets Current assets: Cash and cash equivalents $ 99,647 $ 89,130 Marketable securities 517,929 765,295 Accounts receivable, net 20,112 10,577 Inventory 30,152 32,920 Contract assets 4,104 — Prepaid expenses and other current assets 45,724 44,130 Total current assets 717,668 942,052 Marketable securities 347,254 310,013 Operating lease assets 23,875 30,454 Property and equipment, net 9,946 10,775 Other non-current assets 9,681 3,931 Total assets $ 1,108,424 $ 1,297,225 Liabilities and stockholders’ equity Current liabilities: Accounts payable $ 16,345 $ 18,355 Accrued expenses 34,647 45,459 Operating lease liabilities 19,225 18,392 Total current liabilities 70,217 82,206 Operating lease liabilities, net of current portion 11,946 21,815 Other non-current liabilities 240 90 Total liabilities 82,403 104,111 Stockholders’ equity: Preferred stock, $0.001 par value; 25,000,000 shares authorized; no shares issued or outstanding at June 30, 2026 and December 31, 2025 — — Common stock, $0.001 par value; 125,000,000 shares authorized; 75,821,241 shares issued and 59,604,830 outstanding at June 30, 2026, and 74,665,003 shares issued and 58,448,592 outstanding at December 31, 2025 76 75 Additional paid-in capital 2,591,745 2,555,037 Accumulated other comprehensive (loss) income (1,795) 2,193 Accumulated deficit (761,519) (561,705) Treasury stock, at cost (16,216,411 shares at June 30, 2026 and December 31, 2025) (802,486) (802,486) Total stockholders’ equity 1,026,021 1,193,114 Total liabilities and stockholders’ equity $ 1,108,424 $ 1,297,225 See accompanying Notes to Condensed Consolidated Financial Statements. 1 Table of Contents AGIOS PHARMACEUTICALS, INC. Condensed Consolidated Statements of Operations (Unaudited) Three Months Ended June 30, Six Months Ended June 30, (In thousands, except share and per share data) 2026 2025 2026 2025 Revenues: Product revenue, net $ 44,745 $ 12,455 $ 65,491 $ 21,181 Total revenue 44,745 12,455 65,491 21,181 Operating expenses: Cost of sales $ 2,996 $ 1,702 $ 4,315 $ 2,787 Research and development 100,754 91,940 181,902 164,683 Selling, general and administrative 51,547 45,869 99,851 87,396 Total operating expenses 155,297 139,511 286,068 254,866 Loss from operations (110,552) (127,056) (220,577) (233,685) Interest income, net 9,730 14,513 20,525 30,600 Other income, net 119 523 238 1,776 Net loss $ (100,703) $ (112,020) $ (199,814) $ (201,309) Net loss per share - basic and diluted $ (1.69) $ (1.93) $ (3.38) $ (3.49) Weighted-average number of common shares used in computing net loss per share – basic and diluted 59,488,871 57,932,576 59,137,508 57,697,193 See accompanying Notes to Condensed Consolidated Financial Statements. 2 Table of Contents AGIOS PHARMACEUTICALS, INC. Condensed Consolidated Statements of Comprehensive Loss (Unaudited) Three Months Ended June 30, Six Months Ended June 30, (In thousands) 2026 2025 2026 2025 Net loss $ (100,703) $ (112,020) $ (199,814) $ (201,309) Other comprehensive (loss) income Unrealized (loss) gain on available-for-sale securities (1,481) 290 (3,988) 2,173 Comprehensive loss $ (102,184) $ (111,730) $ (203,802) $ (199,136) See accompanying Notes to Condensed Consolidated Financial Statements. 3 Table of Contents AGIOS PHARMACEUTICALS, INC. Condensed Consolidated Statements of Stockholders' Equity (Unaudited) Common Stock Additional Paid-In Capital Accumulated Other Comprehensive Income (Loss) Accumulated Deficit Treasury Stock Total Stockholders’ Equity (in thousands, except share amounts) Shares Amount Shares Amount Balance at December 31, 2025 74,665,003 $ 75 $ 2,555,037 $ 2,193 $ (561,705) (16,216,411) $ (802,486) $ 1,193,114 Unrealized loss on available-for-sale securities — — — (2,507) — — — (2,507) Common stock issued under stock incentive plan and ESPP 892,746 1 2,077 — — — — 2,078 Stock-based compensation expense — — 15,541 — — — — 15,541 Net loss — — — — (99,111) — — (99,111) Balance at March 31, 2026 75,557,749 $ 76 $ 2,572,655 $ (314) $ (660,816) (16,216,411) $ (802,486) $ 1,109,115 Unrealized loss on available-for-sale securities — — — (1,481) — — — (1,481) Common stock issued under stock incentive plan and ESPP 263,492 — 3,149 — — — — 3,149 Stock-based compensation expense — — 15,941 — — — — 15,941 Net loss — — — — (100,703) — — (100,703) Balance at June 30, 2026 75,821,241 $ 76 $ 2,591,745 $ (1,795) $ (761,519) (16,216,411) $ (802,486) $ 1,026,021 Common Stock Additional Paid-In Capital Accumulated Other Comprehensive Income (Loss) Accumulated Deficit Treasury Stock Total Stockholders’ Equity (in thousands, except share amounts) Shares Amount Shares Amount Balance at December 31, 2024 73,372,696 $ 73 $ 2,493,811 $ (1,518) $ (148,924) (16,216,411) $ (802,486) $ 1,540,956 Unrealized gain on available-for-sale securities — — — 1,883 — — — 1,883 Common stock issued under stock incentive plan and ESPP 730,496 1 1,618 — — — — 1,619 Stock-based compensation expense — — 11,359 — — — — 11,359 Net loss — — — — (89,289) — — (89,289) Balance at March 31, 2025 74,103,192 $ 74 $ 2,506,788 $ 365 $ (238,213) (16,216,411) $ (802,486) $ 1,466,528 Unrealized gain on available-for-sale securities — — — 290 — — — 290 Common stock issued under stock incentive plan and ESPP 151,764 — 65 — — — — 65 Stock-based compensation expense — — 14,692 — — — — 14,692 Net loss — — — — (112,020) — — (112,020) Balance at June 30, 2025 74,254,956 $ 74 $ 2,521,545 $ 655 $ (350,233) (16,216,411) $ (802,486) $ 1,369,555 See accompanying Notes to Condensed Consolidated Financial Statements. 4 Table of Contents AGIOS PHARMACEUTICALS, INC. Condensed Consolidated Statements of Cash Flows (Unaudited) Six Months Ended June 30, (In thousands) 2026 2025 Operating activities Net loss $ (199,814) $ (201,309) Adjustments to reconcile net loss from operations to net cash used in operating activities: Depreciation and amortization 2,713 2,537 Stock-based compensation expense 31,482 26,051 Net accretion of discount on marketable securities (2,271) (3,768) Loss on disposal of property and equipment — 5 Non-cash operating lease expense 6,579 6,094 Expense associated with license agreement 25,000 10,000 Realized gain on investments (95) (2) Changes in operating assets and liabilities: Accounts receivable, net (9,535) (877) Inventory 2,768 (3,232) Contract assets (4,104) — Prepaid expenses and other current and non-current assets (7,344) (3,746) Accounts payable (1,913) 1,084 Accrued expenses and other current liabilities (10,812) (11,572) Income taxes payable — (871) Operating lease liabilities (9,036) (8,228) Other non-current liabilities 150 (779) Net cash used in operating activities (176,232) (188,613) Investing activities Purchases of marketable securities (299,753) (305,700) Proceeds from maturities and sales of marketable securities 508,256 508,894 Payments associated with license agreement (25,000) (10,000) Purchases of property and equipment (1,981) (1,641) Net cash provided by investing activities 181,522 191,553 Financing activities Net proceeds from stock option exercises and employee stock purchase plan 5,227 1,684 Net cash provided by financing activities 5,227 1,684 Net change in cash and cash equivalents 10,517 4,624 Cash and cash equivalents at beginning of the period 89,130 76,247 Cash and cash equivalents at end of the period $ 99,647 $ 80,871 Supplemental disclosure of non-cash investing and financing transactions Additions to property and equipment in accounts payable $ 186 $ 122 Exchanges of marketable securities $ 2,229 $ — Net cash taxes paid $ 74 $ 1,503 See accompanying Notes to Condensed Consolidated Financial Statements. 5 Table of Contents AGIOS PHARMACEUTICALS, INC. Notes to Condensed Consolidated Financial Statements (Unaudited) 1. Overview and Basis of Presentation Note Regarding Certain References in this Quarterly Report on Form 10-Q Throughout this Quarterly Report on Form 10-Q, “Agios,” “the Company,” “we,” “us,” and “our,” and similar expressions, except where the context requires otherwise, refer to Agios Pharmaceuticals, Inc. and its consolidated subsidiaries, and “our Board of Directors” refers to the board of directors of Agios Pharmaceuticals, Inc. In addition, unless otherwise stated or the context indicates otherwise, all references in this Quarterly Report on Form 10-Q to “AQVESME™ (mitapivat)” or “AQVESME™” refer to our U.S. Food and Drug Administration, or FDA, approved medicine for the treatment of anemia in adults with non-transfusion dependent and transfusion-dependent alpha- or beta-thalassemia in the United States; references to “PYRUKYND® (mitapivat)”, “PYRUKYND®”, or “mitapivat” refer to all other commercially available mitapivat products or mitapivat product candidates for which we are exploring further applications and indications, as the context requires. Overview We are a commercial-stage biopharmaceutical company dedicated to redefining the future of rare disease treatment. Fueled by connections, we build trusted partnerships with communities, collaborating to develop and deliver innovative medicines that have the potential to transform lives. With a foundation in hematology, we combine biological expertise with real-world insights to advance a growing pipeline of rare disease medicines that reflect the priorities of the people we serve. We are located in Cambridge, Massachusetts. The lead product candidate in our portfolio, mitapivat, is an activator of both wild-type and mutant pyruvate kinase, or PK, enzymes for the potential treatment of hemolytic anemias. Mitapivat is approved under the brand name AQVESME™ in the United States for the treatment of anemia in adults with non-transfusion dependent and transfusion-dependent alpha- or beta-thalassemia. Mitapivat is approved under the brand name PYRUKYND®: in the United States for the treatment of hemolytic anemia in adults with PK deficiency; in the European Union, or EU, for the treatment of PK deficiency and for the treatment of non-transfusion dependent and transfusion dependent alpha- or beta-thalassemia in adult patients; in the Kingdom of Saudi Arabia for the treatment of adults with non-transfusion dependent and transfusion-dependent alpha- or beta-thalassemia; in the United Arab Emirates for the treatment of non-transfusion-dependent and transfusion-dependent alpha- or beta-thalassemia in adult patients; and in Great Britain for the treatment of PK deficiency in adult patients. We submitted a supplemental New Drug Application, or sNDA, for the U.S. accelerated approval of mitapivat in sickle cell disease, or SCD, in May 2026, which was accepted with priority review by the FDA and granted a Prescription Drug User Fee Act, or PDUFA, goal date of November 1, 2026. To support this accelerated approval pathway, we initiated REIGNITE, a phase 3 confirmatory trial designed to demonstrate the clinical benefit of mitapivat on reducing transfusion burden in patients with SCD aged 12 years or older. Additionally, in the second quarter of 2026 we filed for regulatory approval for SCD in the Kingdom of Saudi Arabia. We are also developing (i) AG-181, our phenylalanine hydroxylase, or PAH, stabilizer for the potential treatment of phenylketonuria, or PKU; (ii) AG-236, an siRNA in-licensed from Alnylam Pharmaceuticals, Inc., or Alnylam, targeting the transmembrane serine protease 6, or TMPRSS6, gene for the potential treatment of polycythemia vera, or PV; and (iii) cevidoplenib, an oral spleen tyrosine kinase, or SYK, inhibitor in-licensed from Oscotec Inc., or Oscotec, for the potential treatment of immune thrombocytopenia, or ITP, and other autoimmune indications. We are subject to risks common to companies in our industry including, but not limited to, uncertainties relating to conducting preclinical and clinical research and development, the manufacture and supply of products for clinical and commercial use, obtaining and maintaining regulatory approvals and pricing and reimbursement for our products, market acceptance, managing global growth and operating expenses, availability of additional capital, competition, obtaining and enforcing patents, stock price volatility, dependence on collaborative relationships and third-party service providers, dependence on key personnel, potential litigation, potential product liability claims and potential government investigations. Oscotec License Agreement On June 1, 2026, we entered into a license agreement with Oscotec, a South Korean biopharmaceutical company, under which Agios acquired the worldwide rights (subject to Oscotec’s right to opt-in to develop and commercialize cevidoplenib in South Korea) to develop, manufacture, and commercialize cevidoplenib as a potential treatment for ITP and other autoimmune 6 Table of Contents indications. Because the acquired assets do not meet the definition of a business in accordance with ASC 805, Business Combinations, Agios will account for the agreement as an asset acquisition. In accordance with the agreement, in the three months ended June 30, 2026, Agios made an up-front payment to Oscotec and recognized in-process research and development of $25.0 million, which was recorded in research and development expense within our Consolidated Statements of Operations and classified as investing activities within our Consolidated Statements of Cash Flows. In addition, Agios is responsible to pay up to $140.0 million in potential development and regulatory milestones in the U.S. and Europe, in addition to sales milestones as well as tiered royalties on future net sales, if any, of licensed products, which may be subject to specified reductions and offsets. Sale of Oncology Business to Servier and Sale of Contingent Payments In March 2021, we completed the sale of our oncology business to Servier Pharmaceuticals, LLC, or Servier. The transaction included the sale of our entire oncology business, including our clinical-stage product candidate vorasidenib, and included a royalty of 15% of U.S. net sales of vorasidenib from the first commercial sale of vorasidenib through loss of exclusivity, or the Vorasidenib Royalty Rights. The Vorasidenib Royalty Rights are referred to as contingent payments and recognized as income when realizable. In May 2024, we entered into a purchase and sale agreement to sell the Vorasidenib Royalty Rights to Royalty Pharma Investments 2019 ICAV, or Royalty Pharma. The sale was contingent upon FDA approval of vorasidenib and other customary closing conditions. Upon consummation of the sale in August 2024, Royalty Pharma acquired 100% of the Vorasidenib Royalty Rights payments made by Servier on account of up to $1.0 billion in U.S. net sales for each calendar year. In addition, any such Vorasidenib Royalty Rights payments made by Servier on account of U.S. net sales in each calendar year in excess of $1.0 billion will be split, with Royalty Pharma having the rights to a 12% earn-out on those excess payments and Agios retaining the rights to a 3% earn-out on those excess payments, or the Retained Earn-Out Rights. Royalty income related to the Retained Earn-Out Rights, if any, will be recognized in the period when realizable. Basis of Presentation The condensed consolidated balance sheet as of June 30, 2026, the condensed consolidated statements of operations, comprehensive loss and stockholders' equity for the three and six months ended June 30, 2026 and 2025, and the condensed consolidated statements of cash flows for the six months ended June 30, 2026 and 2025 are unaudited. The unaudited condensed consolidated financial statements have been prepared on the same basis as the annual financial statements and, in the opinion of our management, reflect all adjustments, which include only normal recurring adjustments, necessary to fairly state our financial position as of June 30, 2026, our results of operations and stockholders' equity for the three and six months ended June 30, 2026 and 2025, and cash flows for the six months ended June 30, 2026 and 2025. The financial data and other financial information disclosed in these notes to the condensed consolidated financial statements related to the three and six-month periods are also unaudited. The results of operations for the three and six months ended June 30, 2026 are not necessarily indicative of the results to be expected for the year ending December 31, 2026 or for any other future annual or interim period. The condensed consolidated balance sheet data as of December 31, 2025 was derived from our audited financial statements, but does not include all disclosures required by U.S. generally accepted accounting principles, or U.S. GAAP. The condensed consolidated interim financial statements should be read in conjunction with the audited consolidated financial statements and notes thereto included in our Annual Report on Form 10-K for the year ended December 31, 2025 that was filed with the Securities and Exchange Commission on February 12, 2026. Our condensed consolidated financial statements include our accounts and the accounts of our wholly owned subsidiaries. All intercompany transactions have been eliminated in consolidation. The condensed consolidated financial statements have been prepared in conformity with U.S. GAAP. Use of Estimates The preparation of our condensed consolidated financial statements requires us to make estimates, judgments and assumptions that may affect the reported amounts of assets, liabilities, equity, revenues and expenses and related disclosure of contingent assets and liabilities. On an ongoing basis we evaluate our estimates, judgments and methodologies. We base our estimates on historical experience and on various other assumptions that we believe are reasonable, the results of which form the basis for making judgments about the carrying values of assets, liabilities and equity and the amount of revenues and expenses. 7 Table of Contents Liquidity As of June 30, 2026, we had cash, cash equivalents and marketable securities of $1.0 billion. Although we have incurred recurring losses and expect to continue to incur losses for the foreseeable future, we expect our cash, cash equivalents and marketable securities to be sufficient to fund current operations for at least the next twelve months from the issuance of the financial statements. If we are unable to raise additional funds through equity or debt financings, we may be required to delay, limit, reduce or terminate product development or future commercialization efforts, or grant rights to develop and market products or product candidates that we would otherwise prefer to develop and market ourselves. 2. Summary of Significant Accounting Policies There have been no material changes to the significant accounting policies previously disclosed in our Annual Report on Form 10-K for the year ended December 31, 2025. Recent Accounting Pronouncements In November 2024, the Financial Accounting Standards Board issued Accounting Standards Update, or ASU, 2024-03, Income Statement – Reporting Comprehensive Income – Expense Disaggregation Disclosures (Subtopic 220-40): Disaggregation of Income Statement Expenses, to improve disclosures around an entity’s expenses. Upon adoption, companies will be required to disclose in the notes to the financial statements a disaggregation of certain expense categories included within the expense captions on the face of the income statement. The standard is effective for annual periods beginning after December 15, 2026 and interim periods beginning after December 15, 2027, with early adoption permitted, and can be applied either prospectively or retrospectively. We plan to adopt the standard in our 2027 annual period and are currently assessing its effect on our financial statement disclosures. 3. Fair Value Measurements We record cash equivalents and marketable securities at fair value. ASC 820, Fair Value Measurements and Disclosures, establishes a fair value hierarchy for those instruments measured at fair value that distinguishes between assumptions based on market data (observable inputs) and our own assumptions (unobservable inputs). The hierarchy consists of three levels: Level 1 – Unadjusted quoted prices in active markets for identical assets or liabilities. Level 2 – Quoted prices for similar assets and liabilities in active markets, quoted prices in markets that are not active, or inputs which are observable, directly or indirectly, for substantially the full term of the asset or liability. Level 3 – Unobservable inputs that reflect our own assumptions about the assumptions market participants would use in pricing the asset or liability in which there is little, if any, market activity for the asset or liability at the measurement date. The following table summarizes our cash equivalents and marketable securities measured at fair value and by level on a recurring basis as of June 30, 2026: (In thousands) Level 1 Level 2 Level 3 Total Cash equivalents $ 30,098 $ 8,643 $ — $ 38,741 Total cash equivalents 30,098 8,643 — 38,741 Marketable securities: U.S. Treasuries — 251,421 — 251,421 Government securities — 145,777 — 145,777 Corporate debt securities — 467,985 — 467,985 Total marketable securities — 865,183 — 865,183 Total cash equivalents and marketable securities $ 30,098 $ 873,826 $ — $ 903,924 Cash equivalents and marketable securities have been initially valued at the transaction price and are subsequently valued, at the end of each reporting period, utilizing third-party pricing services or other observable market data. The pricing services utilize industry standard valuation models, including both income and market-based approaches, and observable market inputs to determine value. After completing our validation procedures, we did not adjust or override any fair value measurements provided by the pricing services as of June 30, 2026. There have been no changes to the valuation methods during the six months ended June 30, 2026, and we had no financial assets or liabilities that were classified as Level 3 at any point during the six months ended June 30, 2026. 8 Table of Contents 4. Marketable Securities Our marketable securities are classified as available-for-sale pursuant to ASC 320, Investments – Debt and Equity Securities, and are recorded at fair value. Unrealized gains and losses are included as a component of accumulated other comprehensive (loss) income in the condensed consolidated balance sheets and statements of stockholders’ equity, and a component of total comprehensive loss in the condensed consolidated statements of comprehensive loss, until realized. Unrealized losses are evaluated for impairment under ASC 326, Financial Instruments - Credit Losses, to determine if the impairment is credit-related or noncredit-related. Credit-related impairment is recognized as an allowance on the condensed consolidated balance sheets with a corresponding adjustment to earnings, and noncredit-related impairment is recognized in other comprehensive income, net of taxes. Realized gains and losses are included in investment income on a specific-identification basis. There were no material realized gains or losses on marketable securities for the three and six months ended June 30, 2026 or 2025. Marketable securities at June 30, 2026 consisted of the following: (In thousands) Amortized Cost Unrealized Gains Unrealized Losses Fair Value Current: U.S. Treasuries $ 96,509 $ 102 $ (8) $ 96,603 Government securities 88,570 4 (61) 88,513 Corporate debt securities 332,977 100 (264) 332,813 Total current 518,056 206 (333) 517,929 Non-current: U.S. Treasuries 155,754 15 (951) 154,818 Government securities 57,467 17 (220) 57,264 Corporate debt securities 135,701 2 (531) 135,172 Total non-current 348,922 34 (1,702) 347,254 Total marketable securities $ 866,978 $ 240 $ (2,035) $ 865,183 Marketable securities at December 31, 2025 consisted of the following: (In thousands) Amortized Cost Unrealized Gains Unrealized Losses Fair Value Current: Certificates of deposit $ 750 $ 1 $ — $ 751 U.S. Treasuries 165,365 463 — 165,828 Government securities 110,182 92 (6) 110,268 Corporate debt securities 487,786 673 (11) 488,448 Total current 764,083 1,229 (17) 765,295 Non-current: U.S. Treasuries 129,738 648 (1) 130,385 Government securities 54,527 31 (10) 54,548 Corporate debt securities 124,767 346 (33) 125,080 Total non-current 309,032 1,025 (44) 310,013 Total marketable securities $ 1,073,115 $ 2,254 $ (61) $ 1,075,308 As of June 30, 2026 and December 31, 2025, we held both current and non-current investments. Investments classified as current have maturities of less than one year. Investments classified as non-current are those that: (i) have a maturity of greater than one year, and (ii) we do not intend to liquidate within the next twelve months, although these funds are available for use and, therefore, are classified as available-for-sale. As of June 30, 2026 and December 31, 2025, we held 134 and 37 debt securities, respectively, that were in an unrealized loss position for less than one year. We did not record an allowance for credit losses as of June 30, 2026 and December 31, 2025 related to these securities. The aggregate fair value of debt securities in an unrealized loss position at June 30, 2026 and 9 Table of Contents December 31, 2025 was $572.7 million and $136.2 million, respectively. There were no individual securities that were in a significant unrealized loss position as of June 30, 2026 and December 31, 2025. We regularly review the securities in an unrealized loss position and evaluate the current expected credit loss by considering factors such as historical experience, market data, issuer-specific factors, and current economic conditions. We do not consider these marketable securities to be impaired as of June 30, 2026 and December 31, 2025. 5. Inventory Inventory, which consists of commercial supply of PYRUKYND® and AQVESME™, consisted of the following: (In thousands) June 30, 2026 December 31, 2025 Raw materials $ 374 $ 88 Work-in-process 32,007 30,253 Finished goods 3,371 2,579 Total inventory $ 35,752 $ 32,920 Balance Sheet Classification: Inventory $ 30,152 $ 32,920 Other non-current assets 5,600 — Total inventory $ 35,752 $ 32,920 Long-term inventory is included in other non-current assets within our condensed consolidated balance sheets. 6. Leases Our building leases are comprised of office and laboratory space under non-cancelable operating leases. These lease agreements have remaining lease terms of approximately two years and contain various clauses for renewal at our option. The renewal options were not included in the calculation of the operating lease assets and the operating lease liabilities as the renewal options are not reasonably certain of being exercised. The lease agreements do not contain residual value guarantees. The components of lease expense and other information related to leases were as follows: Three Months Ended June 30, Six Months Ended June 30, (In thousands) 2026 2025 2026 2025 Operating lease costs $ 3,806 $ 3,806 $ 7,613 $ 7,613 Cash paid for amounts included in the measurement of operating lease liabilities 5,058 4,911 10,070 9,748 We have not entered into any material short-term leases or financing leases as of June 30, 2026. In arriving at the operating lease liabilities as of June 30, 2026 and December 31, 2025, we applied the weighted-average incremental borrowing rate of 5.7% for both periods over a weighted-average remaining lease term of 1.7 and 2.2 years, respectively. As of June 30, 2026, undiscounted minimum rental commitments under non-cancelable leases were as follows: (In thousands) Remaining 2026 $ 8,441 2027 20,755 2028 3,479 Undiscounted minimum rental commitments 32,675 Interest (1,504) Operating lease liabilities $ 31,171 We provided our landlord a security deposit of $2.9 million as security for our leases, which is included within other non-current assets on our condensed consolidated balance sheet. 10 Table of Contents In April 2022, we entered into a long-term sublease agreement for 27,000 square feet of the office space at 64 Sidney Street, Cambridge, Massachusetts, which expired on April 30, 2025. In May 2023, we entered into a long-term sublease agreement for 7,407 square feet of office space on the first floor of 64 Sidney Street, Cambridge, Massachusetts, which expired on July 31, 2025. In July 2025, we entered into a long-term sublease agreement with a new tenant for the same space, which began in November 2025 with the term of the lease running through February 2028. In June 2026, we entered into a long-term sublease agreement for 12,995 square feet of the office space at 38 Sidney Street, Cambridge, Massachusetts, which begins in July 2026 with the term of the lease running through February 2028. We recorded operating sublease income of $0.1 million and $0.5 million for the three months ended June 30, 2026 and 2025, respectively, and $0.2 million and $1.8 million for the six months ended June 30, 2026 and 2025, respectively, in other income, net in the condensed consolidated statements of operations. We hold security deposits from our sublessees of approximately $0.2 million which is recorded within other non-current assets on our condensed consolidated balance sheet. As of June 30, 2026, the future minimum lease payments to be received under the long-term sublease agreements were as follows: (In thousands) Remaining 2026 $ 465 2027 1,054 2028 178 Total $ 1,697 7. Accrued Expenses Accrued expenses consisted of the following: (In thousands) June 30, 2026 December 31, 2025 Accrued compensation $ 14,749 $ 27,264 Accrued research and development costs 10,959 12,081 Accrued professional fees 4,533 3,613 Accrued other 4,406 2,501 Total accrued expenses $ 34,647 $ 45,459 8. Product Revenue We generate product revenue from sales of PYRUKYND® and AQVESME™ in the United States to a limited number of specialty distributors and specialty pharmacy providers, and from sales of PYRUKYND® to Avanzanite and NewBridge outside of the United States, or collectively, the Customers. These Customers subsequently resell PYRUKYND® and AQVESME™ to pharmacies or dispense PYRUKYND® and AQVESME™ directly to patients. In addition to distribution agreements with Customers, we enter into arrangements with healthcare providers and payors that provide for government-mandated and/or privately-negotiated rebates, chargebacks and discounts with respect to the purchase of PYRUKYND® and AQVESME™. The performance obligation related to the sale of PYRUKYND® and AQVESME™ is satisfied and revenue is recognized when the Customer obtains control of the product, which occurs at a point in time, typically upon delivery to the Customer. Product revenue, net, was as follows: 11 Table of Contents Three Months Ended June 30, Six Months Ended June 30, (In thousands) 2026 2025 2026 2025 Product revenue, net United States $ 40,917 $ 12,151 $ 59,768 $ 20,877 Rest of world 3,828 304 5,723 304 Total product revenue, net $ 44,745 $ 12,455 $ 65,491 $ 21,181 Reserves for Variable Consideration Revenues from product sales are recorded at the net sales price, or transaction price, which includes estimates of variable consideration for which reserves are established and result from contractual adjustments, government rebates, returns and other allowances that are offered within the contracts with our Customers, healthcare providers, payors and other indirect customers relating to the sale of our products. Contractual Adjustments We generally provide Customers with discounts, including prompt pay discounts, and allowances that are explicitly stated in the contracts and are recorded as a reduction of revenue in the period the related product revenue is recognized. In addition, we receive sales order management, data and distribution services from certain Customers. Chargebacks and discounts represent the estimated obligations resulting from contractual commitments to sell products to qualified healthcare providers at prices lower than the list prices charged to Customers who directly purchase the product from us. Customers charge us for the difference between what they pay for the product and the ultimate selling price to the qualified healthcare providers. These reserves are estimated using the expected value method, based upon a range of possible outcomes that are probability-weighted for the estimated channel mix and are established in the same period that the related revenue is recognized, resulting in a reduction of product revenue. Government Rebates Government rebates include Medicare, TriCare, and Medicaid rebates, which we estimate using the expected value method, based upon a range of possible outcomes that are probability-weighted for the estimated payor mix. These reserves are recorded in the same period the related revenue is recognized, resulting in a reduction of product revenue. For Medicare, we also estimate the number of patients for whom we will owe an additional liability under the Medicare Part D Manufacturer Discount Program. Returns / Replacement / Other Allowances We estimate the amount of product sales that may be returned by Customers or replaced by Agios, or other allowances for revenue not expected to be sold by Customers, and record these estimates as a reduction of revenue in the period the related product revenue is recognized. We currently estimate product return and replacement liabilities, and the revenue reserve related to other allowances using the expected value method, based on available industry data, including our visibility into the inventory remaining in the distribution channel. The following table summarizes balances and activity in each of the product revenue allowance and reserve categories for the six months ended June 30, 2026: (In thousands) Contractual Adjustments Government Rebates Returns/ Replacement/ Other Total Balance at December 31, 2025 $ 182 $ 1,274 $ 1,040 $ 2,496 Current provisions relating to sales in the current year 1,817 3,738 4,519 10,074 Adjustments relating to prior years — (113) (370) (483) Payments/returns relating to sales in the current year (1,459) (1,016) — (2,475) Payments/returns relating to sales in the prior years (174) (895) (16) (1,085) Balance at June 30, 2026 $ 366 $ 2,988 $ 5,173 $ 8,527 Total revenue-related reserves above, included in our condensed consolidated balance sheets, are summarized as follows: 12 Table of Contents (In thousands) June 30, 2026 December 31, 2025 Reduction of accounts receivable $ 369 $ 174 Reduction of contract assets 3,865 — Component of accrued expenses 4,293 2,322 Total revenue-related reserves $ 8,527 $ 2,496 The following table presents changes in our contract assets during the six months ended June 30, 2026: (In thousands) December 31, 2025 Additions Deductions June 30, 2026 Accounts receivable, net (1) $ 10,577 $ 67,126 $ (57,591) $ 20,112 Contract assets (2) — 4,104 — 4,104 Total contract assets $ 10,577 $ 71,230 $ (57,591) $ 24,216 (1) Additions to accounts receivable, net relate to amounts billed to Customers for product sales and deductions from accounts receivable, net primarily relate to collection of receivables during the reporting period. (2) Additions to contract assets relate to amounts unbilled to Customers for net product sales, and deductions from contract assets relate to amounts billed to Customers for product sales. 9. Share-Based Payments 2023 Stock Incentive Plan and Inducement Grants In June 2023, our stockholders approved the 2023 Stock Incentive Plan, or the 2023 Plan. The 2023 Plan provides for the grant of incentive stock options, nonstatutory stock options, stock appreciation rights, restricted stock awards, restricted stock units, or RSUs, performance-based stock units, or PSUs, and other stock-based awards to employees, advisors, consultants and non-employee directors. Following the adoption of the 2023 Plan, we ceased granting equity awards under the 2013 Stock Incentive Plan, or the 2013 Plan. Any outstanding equity awards that were previously granted under the 2013 Plan continue to be governed by their terms. Following adoption of the 2013 Plan, we ceased granting equity awards under the 2007 Stock Incentive Plan, or the 2007 Plan. There are no outstanding equity awards under the 2007 Plan. In connection with the start of employment of our Chief Executive Officer and Chief Financial Officer in 2022, our Chief Commercial Officer in 2023, and our Chief Corporate Development and Strategy Officer in March 2025, our Board of Directors granted each of them equity awards in the form of stock options, RSUs and PSUs, which awards were made outside our equity incentive plans as inducements material to their respective entry into employment with us in accordance with Nasdaq Listing Rule 5635(c)(4). As of June 30, 2026, the maximum number of shares reserved under the 2013 Plan, the 2023 Plan and the inducement grants described above was 13,242,570, and we had 4,014,743 shares available for future issuance under the 2023 Plan. Stock options The following table presents stock option activity for the six months ended June 30, 2026: Number of Stock Options Weighted-AverageExercise Price Outstanding at December 31, 2025 6,113,063 $ 39.62 Granted 851,777 29.98 Exercised (115,910) 28.77 Cancelled/Forfeited (168,230) 46.41 Expired (128,627) 42.25 Outstanding at June 30, 2026 6,552,073 $ 38.33 Exercisable at June 30, 2026 4,629,494 $ 41.19 Vested and expected to vest at June 30, 2026 6,552,073 $ 38.33 At June 30, 2026, there was approximately $32.2 million of total unrecognized compensation expense related to unvested stock option awards, which we expect to recognize over a weighted-average period of approximately 2.60 years. 13 Table of Contents Restricted stock units The following table presents RSU activity for the six months ended June 30, 2026: Number of Stock Units Weighted-AverageGrant Date Fair Value Unvested shares at December 31, 2025 2,007,463 $ 32.03 Granted 1,258,034 29.16 Vested (871,391) 29.87 Forfeited (207,202) 32.19 Unvested shares at June 30, 2026 2,186,904 $ 31.22 As of June 30, 2026, there was approximately $54.1 million of total unrecognized compensation expense related to RSUs, which we expect to recognize over a weighted-average period of approximately 2.04 years. Performance-based stock units The following table presents PSU activity for the six months ended June 30, 2026: Number of Stock Units Weighted-AverageGrant Date Fair Value Unvested shares at December 31, 2025 376,978 $ 32.55 Granted 83,500 29.20 Vested (103,128) 31.69 Unvested shares at June 30, 2026 357,350 $ 32.02 Stock-based compensation expense associated with PSUs is recognized if the underlying performance condition is considered probable of achievement using our management’s best estimates. For PSUs that also have a service period requirement, stock-based compensation expense is recognized over the service period once the underlying performance condition is considered probable of achievement using our management's best estimates. Included in unvested shares were 61,812 shares with performance conditions that were considered probable of achievement at June 30, 2026, but which also have a service period requirement until December 31, 2027. As of June 30, 2026, there was approximately $1.1 million of total unrecognized compensation expense related to these PSUs. As of June 30, 2026, there was $9.4 million of total unrecognized compensation expense related to PSUs with performance-based vesting criteria that are considered not probable of achievement. Market-based stock units We have issued certain equity awards that contain market-based vesting conditions, in which shares of stock are earned at vesting based on total shareholder return compared to an industry stock index. The fair value of market-based stock units, or MSUs, is estimated using a Monte Carlo simulation model. Assumptions and estimates utilized in the model include the risk-free interest rate, dividend yield, expected stock volatility and the service period. The following table presents MSU activity for the six months ended June 30, 2026: Number of Stock Units Weighted-AverageGrant Date Fair Value Unvested shares at December 31, 2025 — $ — Granted 131,500 49.34 Unvested shares at June 30, 2026 131,500 $ 49.34 As of June 30, 2026, there was $5.7 million of unrecognized compensation expense related to MSUs with market-based vesting criteria, which we expect to recognize over a weighted-average period of approximately 2.50 years. Amended and Restated 2013 Employee Stock Purchase Plan In June 2013, our Board of Directors adopted, and in July 2013 our stockholders approved, the 2013 Employee Stock Purchase Plan, or 2013 ESPP, which was further amended and restated by our Board of Directors in December 2024. We issued and sold 65,809 and 52,092 shares of common stock during the six months ended June 30, 2026 and 2025, respectively, under the 2013 14 Table of Contents ESPP. The 2013 ESPP provides participating employees with the opportunity to purchase up to an aggregate of 2,363,636 shares of our common stock. As of June 30, 2026, we had 1,384,142 shares of common stock available for future issuance under the 2013 ESPP. Stock-based compensation expense Stock-based compensation expense by award type included within the condensed consolidated statements of operations is as follows: Three Months Ended June 30, Six Months Ended June 30, (In thousands) 2026 2025 2026 2025 Stock options $ 5,951 $ 4,622 $ 10,452 $ 9,022 Restricted stock units 7,947 7,507 15,145 14,191 Performance-based stock units 964 2,188 4,232 2,188 Market-based stock units 570 — 764 — Employee stock purchase plan 509 375 889 650 Total stock-based compensation expense $ 15,941 $ 14,692 $ 31,482 $ 26,051 Expenses related to stock options and stock-based awards were allocated as follows in the condensed consolidated statements of operations: Three Months Ended June 30, Six Months Ended June 30, (In thousands) 2026 2025 2026 2025 Research and development expense $ 6,815 $ 5,336 $ 12,510 $ 9,940 Selling, general and administrative expense 9,126 9,356 18,972 16,111 Total stock-based compensation expense $ 15,941 $ 14,692 $ 31,482 $ 26,051 10. Net Loss per Share Basic net loss per share is calculated by dividing net loss by the weighted-average shares outstanding during the period, without consideration for common stock equivalents. Diluted net loss per share is calculated by adjusting the weighted-average shares outstanding for the dilutive effect of common stock equivalents outstanding for the period, determined using the treasury stock method. For purposes of the dilutive net loss per share calculation, stock options, RSUs, PSUs and MSUs for which the performance and market vesting conditions, respectively, have been deemed probable, and 2013 ESPP shares are considered to be common stock equivalents, while PSUs and MSUs with performance and market vesting conditions, respectively, that were not deemed probable as of June 30, 2026 are not considered to be common stock equivalents. We utilize the control number concept in the computation of diluted earnings per share to determine whether potential common stock equivalents are dilutive. The control number used is net loss from continuing operations. The control number concept requires that the same number of potentially dilutive securities applied in computing diluted earnings per share from continuing operations be applied to all other categories of income or loss, regardless of their anti-dilutive effect on such categories. Since we had a net loss for all periods presented, no dilutive effect was recognized in the calculation of loss per share and basic and diluted net loss per share was the same for those periods. The following common stock equivalents were excluded from the calculation of diluted net loss per share applicable to common stockholders for the periods indicated because including them would have had an anti-dilutive effect: Three and Six Months Ended June 30, 2026 2025 Stock options 6,552,073 6,424,575 Restricted stock units 2,186,904 2,096,123 Performance-based stock units 61,812 — Employee stock purchase plan shares 35,327 45,571 Total common stock equivalents 8,836,116 8,566,269 15 Table of Contents 11. Segment Information Operating segments are identified as components of an enterprise about which separate discrete financial information is available for evaluation by the chief operating decision maker, or CODM, or decision-making group in making decisions on how to allocate resources and assess performance. Our CODM is our CEO. Our CEO views our operations and manages our business as one operating segment, which derives its revenues from the development and commercialization of therapies for patients with rare diseases. Our CEO manages and allocates resources to the operations of our company on a total company basis by assessing the overall level of resources available and how to best deploy these resources across functions and research and development projects that are in line with our long-term company-wide strategic goals. In making these decisions, our CEO uses consolidated financial information for purposes of evaluating performance, forecasting future period financial results, allocating resources and setting incentive targets. The CODM performs this assessment based on our consolidated net (loss) income. Through this analysis, the CODM assesses performance by comparing actual consolidated net (loss) income versus the budget, and then decides how to allocate resources to invest in our research and development programs. The measure of segment assets is reported on the condensed consolidated balance sheets as total assets. The following table contains additional information on our consolidated revenue and net loss, including significant segment expenses: Three Months Ended June 30, Six Months Ended June 30, (In thousands) 2026 2025 2026 2025 Product revenue, net - U.S. $ 40,917 $ 12,151 $ 59,768 $ 20,877 Product revenue, net - Rest of world 3,828 304 5,723 304 PK activator (PYRUKYND®/AQVESME™) direct expenses - research and development (25,849) (29,809) (49,754) (51,130) Compensation and related expenses - research and development (30,352) (27,594) (67,141) (60,584) Total selling, general and administrative expenses (51,547) (45,869) (99,851) (87,396) Other segment items* (37,700) (21,203) (48,559) (23,380) Net loss $ (100,703) $ (112,020) $ (199,814) $ (201,309) *Other segment items primarily include cost of sales, other research and development expenses, and interest income. 16 Table of Contents