AGIOS PHARMACEUTICALS, INC.

Results of Operations

Comparison of the three and nine months ended September 30, 2026 and 2025

Revenues

Total Revenue - Three Months Ended September 30, 2026 vs. Three Months Ended September 30, 2025 – The increase in total revenue of $42.5 million for the three months ended September 30, 2026 compared to the three months ended September 30, 2025 was primarily due to an increase of $36.4 million in United States product revenue, principally driven by AQVESME® sales, which we began recognizing product revenue for in the first quarter of 2026.

Total Revenue - Nine Months Ended September 30, 2026 vs. Nine Months Ended September 30, 2025 – The increase in total revenue of $86.8 million for the nine months ended September 30, 2026 compared to the nine months ended September 30, 2025 was due to an increase of $75.3 million in United States product revenue and an increase of $11.5 million in rest of world product revenue. The increase in United States product revenue was primarily due to AQVESME® sales, for which we began recognizing product revenue in the first quarter of 2026, and increased volume associated with PYRUKYND®. The increase in rest of world product revenue was primarily due to sales associated with the Avanzanite Agreement and increased volume associated with the NewBridge Agreement discussed above in Overview.

Total Operating Expenses

Total Operating Expenses - Three Months Ended September 30, 2026 vs. Three Months Ended September 30, 2025– The increase in total operating expenses of $2.8 million for the three months ended September 30, 2026 compared to the three months ended September 30, 2025 was primarily due to an increase in selling, general and administrative expenses of $15.3 million, driven by an increase in commercial-related activities as we execute our launch of AQVESME® in thalassemia and prepare for our potential launch of mitapivat in SCD, partially offset by a decrease in research and development expenses of $13.3 million, which is described below under Research and Development Expenses.

Total Operating Expenses - Nine Months Ended September 30, 2026 vs. Nine Months Ended September 30, 2025– The increase in total operating expenses of $34.0 million for the nine months ended September 30, 2026 compared to the nine months ended September 30, 2025 was primarily due to an increase in selling, general and administrative expenses of $27.7 million, driven by an increase in commercial-related activities as we execute our launch of AQVESME® in thalassemia and prepare for our potential launch of mitapivat in SCD, and an increase in stock compensation expense.

Research and Development Expenses

Our research and development expenses, by major program, are outlined in the table below:

Total Research and Development Expenses - Three Months Ended September 30, 2026 vs. Three Months Ended September 30, 2025– The decrease in total research and development expenses of $13.3 million for the three months ended September 30, 2026 compared to the three months ended September 30, 2025 was primarily due to a $10.4 million decrease in our direct expenses. The decrease in direct expenses was primarily due to a decrease in PYRUKYND®/AQVESME® costs of $8.8 million driven principally by lower process development expenses and lower clinical trial costs associated with thalassemia, and a decrease in tebapivat costs of $2.6 million primarily due to lower process development expenses.

Total Research and Development Expenses - Nine Months Ended September 30, 2026 vs. Nine Months Ended September 30, 2025– The increase in total research and development expenses of $3.9 million for the nine months ended September 30, 2026 compared to the nine months ended September 30, 2025 was due to a $2.7 million increase in our indirect expenses and a $1.2 million increase in our direct expenses. The increase in our indirect expenses was primarily due to higher compensation and related expenses driven principally by an increase in stock compensation expenses. The increase in direct expenses was primarily due to an increase in in-process research and development of $15.0 million, driven by the $25.0 million up-front payment associated with the agreement with Oscotec discussed above under Overview, partially offset by a decrease in PYRUKYND®/AQVESME® costs of $10.2 million, principally driven by lower clinical trial costs associated with PK deficiency and lower process development expenses, and a decrease in tebapivat costs of $3.6 million principally driven by lower clinical trial costs associated with LR-MDS.

Other Income and Expense

Other Income and Expense - Three Months Ended September 30, 2026 vs. Three Months Ended September 30, 2025– The increase in royalty income from gain on sale of oncology business was due to royalty income related to the Retained Earn-Out Rights discussed above in Overview. The decrease in interest income, net was primarily due to a lower investment balance in the three months ended September 30, 2026 compared to the three months ended September 30, 2025.

Other Income and Expense - Nine Months Ended September 30, 2026 vs. Nine Months Ended September 30, 2025– The increase in royalty income from gain on sale of oncology business was due to royalty income related to the Retained Earn-Out Rights discussed above in Overview. The decrease in interest income, net was primarily due to a lower investment balance in the nine months ended September 30, 2026 compared to the nine months ended September 30, 2025.

Net Loss

Net Loss - Three Months Ended September 30, 2026 vs. Three Months Ended September 30, 2025– The decrease in net loss for the three months ended September 30, 2026 compared to the three months ended September 30, 2025 was primarily driven by the increase in product revenue discussed above under Revenuesand the decrease in research and development expenses discussed above under Research and Development Expenses, partially offset by the increase in selling, general and administrative expenses discussed above under Total Operating Expensesand the decrease in interest income, net discussed above in Other Income and Expense.

Net Loss - Nine Months Ended September 30, 2026 vs. Nine Months Ended September 30, 2025– The decrease in net loss for the nine months ended September 30, 2026 compared to the nine months ended September 30, 2025 was primarily driven by the increase in product revenue discussed above under Revenues, partially offset by the increase in selling, general and administrative expenses discussed above under Total Operating Expenses and the decrease in interest income, net discussed above in Other Income and Expense.

Liquidity and Capital Resources

Sources of Liquidity

Since our inception, and through March 2021, we financed our operations primarily through proceeds from the sale of our royalty rights, commercial sales of TIBSOVO®, funding received from our collaboration agreements, private placements of our preferred stock, our initial public offering of our common stock and concurrent private placement of common stock to an affiliate of Celgene, and our follow-on public offerings. Following the sale of our oncology business to Servier in March 2021, we have financed and expect to continue to finance our operations primarily through cash on hand, potential royalty payments with respect to the Retained Earn-Out Rights, the actual and potential future sales of PYRUKYND® and AQVESME® and, potentially, collaborations, strategic alliances, licensing arrangements and other nondilutive strategic transactions. In addition, we may pursue opportunistic debt offerings, and equity or equity-linked offerings.

In March 2021, we completed the sale of our oncology business to Servier. The transaction included the sale of our entire oncology business, including our clinical-stage product candidate vorasidenib and 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. 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 will be recognized in the period when realizable. We recorded $3.0 million related to the Retained Earn-Out Rights within the royalty income from gain on sale of oncology business line item in our condensed consolidated statements of operations for the three and nine months ended September 30, 2026.

Our cash, cash equivalents and marketable securities balance was $907.0 million at September 30, 2026. The Retained Earn-Out Rights discussed above are our only committed potential external sources of funds. We cannot predict what further success, if any, Servier may have in the United States with respect to the sale of vorasidenib, and consequently, we cannot estimate the amount of payments, if any, we may in the future receive on account of the Retained Earn-Out Rights.

Cash Flows

The following table provides information regarding our cash flows for the nine months ended September 30, 2026 and 2025:

Net cash used in operating activities. Cash used in operating activities of $235.5 million during the nine months ended September 30, 2026 was primarily due to operating expenses driven by research and development costs described above under Research and Development Expenses, partially offset by cash received from product revenues of $106.8 million and interest income of $32.3 million.

Cash used in operating activities of $276.8 million during the nine months ended September 30, 2025 was primarily due to operating expenses driven by research and development costs described above under Research and Development Expenses, partially offset by cash received from interest income of $45.8 million and product revenues of $35.8 million.

Net cash provided by investing activities. Cash provided by investing activities of $265.5 million during the nine months ended September 30, 2026 was primarily due to higher proceeds from maturities and sales of marketable securities than purchases of marketable securities.

Cash provided by investing activities of $287.1 million during the nine months ended September 30, 2025 was primarily due to higher proceeds from maturities and sales of marketable securities than purchases of marketable securities.

Net cash provided by financing activities. Cash provided by financing activities of $9.4 million during the nine months ended September 30, 2026 was due to net proceeds received from stock option exercises and purchases made pursuant to our Amended and Restated 2013 Employee Stock Purchase Plan, or 2013 ESPP.

Cash provided by financing activities of $6.1 million during the nine months ended September 30, 2025, was due to net proceeds received from stock option exercises and purchases made pursuant to our 2013 ESPP.

Funding Requirements

We expect our expenses to increase as we continue the research, development and clinical trials of, seek marketing approvals for, and commercialize our product candidates in our portfolio, including as we continue to commercialize PYRUKYND® and AQVESME® for their approved indications. If we obtain additional marketing approvals for mitapivat in SCD or in other indications, or for any of our other product candidates, we expect to incur significant commercialization expenses related to product sales, marketing, manufacturing and distribution.

We expect that our existing cash, cash equivalents and marketable securities as of September 30, 2026, together with anticipated product revenue and interest income, will provide the financial independence to execute the U.S. commercial launch of AQVESME® in thalassemia, prepare for the potential U.S. commercial launch of mitapivat in SCD, and progress our pipeline. Our expectations regarding our long-term funding requirements are based on assumptions that may prove to be wrong, and we may need additional capital resources to fund our operating plans and capital expenditure requirements.

Our future capital requirements will depend on many factors, including:

•the amount and timing of future revenue received from commercial sales of PYRUKYND®, AQVESME® or any of our other product candidates for which we may receive marketing approval;

•the amount of future payments, if any, we may receive on account of the Retained Earn-Out Rights;

•the costs and timing of our ongoing and future commercialization activities, including product manufacturing, sales, marketing and distribution for PYRUKYND® and AQVESME® in the approved jurisdictions and indications and for any product candidate for which we may receive approval;

•the scope, progress, results and costs of preclinical development, laboratory testing and clinical trials for our product candidates;

•the costs associated with in-licensing or acquiring assets for pipeline growth, including the amount and timing of future milestone and royalty payments potentially payable to Alnylam and Oscotec pursuant to the respective license agreements;

•the costs, timing and outcome of regulatory review of our product candidates;

•the costs of preparing, filing and prosecuting patent applications, maintaining and enforcing our intellectual property rights and defending intellectual property-related claims;

•our ability to establish and maintain collaborations on favorable terms, if at all;

•our ability to successfully execute on our strategic plans;

•operational delays due to public health epidemics; and

•operational delays, disruptions and/or increased costs associated with global economic and political developments.

Until such time, if ever, as we can generate substantial product revenue, we expect to finance our cash needs primarily through cash on hand, potential royalty payments with respect to the Retained Earn-Out Rights, the actual and potential future sales of PYRUKYND® and AQVESME® and, potentially, collaborations, strategic alliances, licensing arrangements and other nondilutive strategic transactions. In addition, we may pursue opportunistic debt offerings, and equity or equity-linked offerings. We do not have any committed external source of funds other than the Retained Earn-Out Rights and we cannot be certain we will ever receive any future payments as a result of the Retained Earn-Out Rights. To the extent that we raise additional capital through the sale of equity or convertible debt securities, the ownership interest of our stockholders will be diluted, and the terms of these securities may include liquidation or other preferences that adversely affect the rights of our common stockholders. Debt financing, if available, may involve agreements that include covenants limiting or restricting our ability to take specific actions, such as incurring additional debt, selling or licensing our assets, making capital expenditures or declaring dividends.

If we raise funds through collaborations, strategic alliances or licensing arrangements with third parties, we may have to relinquish valuable rights to our technologies, future revenue streams, research programs or product candidates, or grant licenses on terms that may not be favorable to us. If we are unable to raise additional funds through equity or debt financings when needed or on attractive terms, we may be required to delay, limit, reduce or terminate our product development or future commercialization efforts, or grant rights to develop and market product candidates that we would otherwise prefer to develop and market ourselves.

Contractual Obligations

In June 2026, Agios entered into a license agreement with Oscotec as discussed above under Overview. Under the license agreement, Agios is responsible to pay up to $140.0 million in potential development and regulatory milestones, in addition to sales milestones as well as tiered royalties on annual net sales, if any, of licensed products, which may be subject to specified reductions and offsets.

During the nine months ended September 30, 2026, there were no other material changes to our contractual obligations and commitments described under Management's Discussion and Analysis of Financial Condition and Results of Operations in our Annual Report on Form 10-K for the year ended December 31, 2025.