Apogee Therapeutics, Inc.

The following table summarizes our consolidated statements of operations for the periods presented (in thousands):

The following table summarizes our research and development expenses incurred for the periods presented (in thousands):

Research and development expenses for the three months ended September 30, 2025 and 2024 were $54.2 million and $45.7 million, respectively. The increase of $8.5 million was primarily driven by further development of our APG777 program and increases in personnel costs and equity-based compensation, associated with the growth in our research and development team, partially offset by decreases in expenses related to the APG990/APG279, APG333/APG273 and APG808 programs.

Research and development expense related to the APG777 program increased by $7.8 million in the three months ended September 30, 2025, compared to the three months ended September 30, 2024, primarily driven by an increase in clinical trial-related expenses and clinical manufacturing activities to support our Phase 1 and Phase 2 clinical trials. Research and development expense related to the APG990/APG279 program decreased by $1.4 million in the three months ended September 30, 2025, compared to the three months ended September 30, 2024, primarily due to a decrease in expenses incurred under the Option Agreements and License Agreements, including a milestone payment of $2.0 million to Paragon in August 2024, related to the first dosing of human participants in a Phase 1 clinical trial, partially offset by an increase in clinical trial expenses. Research and development expense related to the APG333/APG273 program decreased by $7.3 million in the three months ended September 30, 2025, compared to the three months ended September 30, 2024, primarily due to a reduction in clinical manufacturing activities and a decrease in preclinical research and development expenses. Research and development expense related to the APG808 program decreased by $1.6 million in the three months ended September 30, 2025, compared to the three months ended September 30, 2024, primarily driven by a decrease in clinical manufacturing expenses.

External-discovery related costs and other expenses increased by $1.0 million in the three months ended September 30, 2025, compared to the three months ended September 30, 2024, primarily driven by an increase in professional service fees. Personnel-related expenses and equity-based compensation increased by $6.7 million and $3.3 million, respectively, in the three months ended September 30, 2025, compared to the three months ended September 30, 2024, primarily due to increased headcount and an increase in the fair value of equity awards granted.

General and Administrative Expense

The following table summarizes our general and administrative expenses for the periods presented (in thousands):

General and administrative expenses for the three months ended September 30, 2025 were $17.1 million, compared to $13.0 million for the three months ended September 30, 2024. The increase of $4.1 million was primarily due to increases in personnel-related expenses and equity-based compensation of $2.5 million and $2.8 million, respectively, primarily driven by increased headcount and an increase in the fair value of equity awards granted, partially offset by a $1.2 million decrease in legal and professional fees. The increase in total general and administrative expense was the result of the expansion of our operations to support the growth in our business.

Other Income, Net

Interest income decreased $3.4 million for the three months ended September 30, 2025, compared to the three months ended September 30, 2024, which was primarily related to interest on our cash, cash equivalents and marketable securities.

Comparison of the Nine Months Ended September 30, 2025 and 2024

The following table summarizes our consolidated statements of operations for the periods presented (in thousands):

The following table summarizes our research and development expenses incurred for the periods presented (in thousands):

Research and development expenses for the nine months ended September 30, 2025 and 2024 were $156.3 million and $107.6 million, respectively. The increase of $48.7 million was primarily driven by further development of our APG777 program and increases in personnel costs and equity-based compensation, associated with the growth in our research and development team, partially offset by decreases in expenses related to the APG990/APG279, APG333/APG273 and APG808 programs.

Research and development expense related to the APG777 program increased by $30.3 million in the nine months ended September 30, 2025, compared to the nine months ended September 30, 2024, primarily driven by an increase in clinical trial-related expenses and clinical manufacturing activities to support our ongoing clinical trials. Research and development expense related to the APG990/APG279 program decreased by $6.3 million in the nine months ended September 30, 2025, compared to the nine months ended September 30, 2024, primarily due to a reduction in clinical manufacturing activities and a decrease in expenses incurred under the Option Agreements and License Agreements, which included milestone payments of $1.0 million and $2.0 million to Paragon, related to the nomination of a development candidate in May 2024, and the first dosing of human participants in a Phase 1 clinical trial in August 2024, respectively, partially offset by an increase in clinical trial expenses. Research and development expense related to the APG333/APG273 program decreased by $11.1 million in the nine months ended September 30, 2025, compared to the nine months ended September 30, 2024, primarily due to a reduction in clinical manufacturing activities and a decrease in expenses incurred under the Option Agreements and License Agreements, including a payment of $2.0 million to Paragon in January 2024 for the finalization of the TSLP research plan, partially offset by an increase in clinical trial expenses. Research and development expense related to the APG808 program decreased by $5.0 million in the nine months ended September 30, 2025, compared to the nine months ended September 30, 2024, primarily driven by a decrease in expenses incurred under the Option Agreements and License Agreements, including a milestone payment of $2.0 million to Paragon in March 2024 for the first dosing of a human patient in a Phase 1 trial, as well as decreases in clinical trial and clinical manufacturing expenses.

External-discovery related costs and other expenses increased by $6.1 million in the nine months ended September 30, 2025, compared to the nine months ended September 30, 2024, primarily due to increases in non-program specific research and development expenses, travel and other employee related expenses, and professional service fees. Personnel-related expenses and equity-based compensation increased by $24.4 million and $10.1 million, respectively, in the nine months ended September 30, 2025 compared to the nine months ended September 30, 2024, primarily due to increased headcount and an increase in the fair value of equity awards granted.

General and Administrative Expense

The following table summarizes our general and administrative expenses for the periods presented (in thousands):

General and administrative expenses for the nine months ended September 30, 2025 were $51.3 million, compared to $33.4 million for the nine months ended September 30, 2024. The increase of $17.9 million was primarily due to an increase in personnel costs and equity-based compensation of $8.0 million and $8.5 million, respectively, primarily driven by increased headcount and an increase in the fair value of equity awards granted. Additionally, other expenses increased by $2.4 million, primarily due to increases in rent expense, as well as travel and other employee related expenses. The increase in total general and administrative expenses was the result of the expansion of our operations to support the growth in our business.

Other Income, Net

Interest income decreased by $4.8 million for the nine months ended September 30, 2025 compared to the nine months ended September 30, 2024, which was primarily related to interest on our cash, cash equivalents and marketable securities.

Liquidity and Capital Resources

Sources of Liquidity

Since our inception, we have incurred significant losses. We have not yet commercialized any of our product candidates, which are in various phases of early-stage development, and we do not expect to generate revenue from sales of any of our product candidates for several years, if at all. To date, we have financed our operations with the proceeds from the issuance of preferred units and the sale of common stock in our IPO, our March 2024 Offering, our ATM (as defined below) and our October 2025 Offering. As of September 30, 2025, we had cash and cash equivalents of $107.9 million, marketable securities of $419.4 million and long-term marketable securities of $61.6 million (excluding proceeds from our October 2025 Offering).

Prior to our IPO, we received gross proceeds of $169.0 million from sales of our preferred units. In connection with our IPO in July 2023, we issued and sold an aggregate of 20,297,500 shares of common stock (inclusive of 2,647,500 shares pursuant to the exercise in full of the underwriters’ option to purchase additional shares) at a price of $17.00 per share for aggregate net proceeds of $315.4 million, after deducting underwriting discounts and commissions and other offering expenses. In connection with our March 2024 Offering, we issued and sold an aggregate of 7,790,321 shares of common stock (inclusive of 1,016,128 shares pursuant to the exercise in full of the underwriters’ option to purchase additional shares) at a public offering price of $62.00 per share, for aggregate net proceeds of $450.0 million after deducting underwriting discounts and commissions and other offering expenses.

In August 2024, we entered into an Open Market Sale Agreement (the “Sale Agreement”) with Jefferies LLC (the “Sales Agent”), pursuant to which we may offer and sell shares of common stock up to a maximum aggregate offering price of $300.0 million, from time to time, through an at the market offering program (the “ATM”). In December 2024, we sold 926,049 shares of common stock under the ATM at a price per share of $48.50 resulting in net proceeds of $43.6 million. In the three months ended September 30, 2025, we sold 527,437 shares of common stock under the ATM for gross proceeds of $20.0 million, less commissions and other offering expenses of $0.6 million. As of September 30, 2025, $235.1 million remained available for sale under the Sale Agreement.

On October 10, 2025, pursuant to our Registration Statement on Form S-3, which became effective in August 2024 (File No 333-281503), we issued and sold an aggregate of 8,048,782 shares of common stock (inclusive of 1,097,561 shares of common stock pursuant to the exercise in full of the underwriters’ option to purchase additional shares) at a public offering price of $41.00 per share, and, in lieu of common stock to certain investors, pre-funded warrants to purchase up to 365,853 shares of common stock at a public offering price of $40.99999 per pre-funded warrant. The pre-funded warrants have an exercise price of $0.00001 per share and are exercisable immediately. The aggregate net proceeds from the offering were $324.1 million after deducting underwriting discounts and commissions and other offering expenses payable by the Company.

Cash Flows

The following table provides information regarding our cash flows for the periods presented (in thousands):

Net Cash used in Operating Activities

Cash used in operating activities resulted primarily from our net losses adjusted for non-cash charges and changes in components of operating assets and liabilities, which are generally attributable to timing of payments, and the related effect on certain account balances, operational and strategic decisions and contracts to which we may be a party.

For the nine months ended September 30, 2025, operating activities used $164.8 million of cash, primarily due to a net loss of $186.5 million, net changes in our operating assets and liabilities of $10.6 million and amortization of discounts on marketable securities of $5.8 million. This was partially offset by non-cash charges of $34.3 million and $2.7 million for equity-based compensation and lease expense, respectively.

For the nine months ended September 30, 2024, operating activities used $103.5 million of cash, primarily due to a net loss of $114.9 million and amortization of discounts on marketable securities of $9.3 million. This was partially offset by a non-cash charge of $15.7 million for equity-based compensation and net changes in operating assets and liabilities of $4.0 million.

Net Cash provided by (used in) Investing Activities

For the nine months ended September 30, 2025, net cash provided by investing activities of $109.1 million was related to $367.3 million in maturities of marketable securities, partially offset by the $253.2 million purchase of marketable securities and $5.1 million purchase of property and equipment.

For the nine months ended September 30, 2024, net cash used in investing activities of $346.8 million was primarily related to the $588.9 million purchase of marketable securities, partially offset by $243.2 million in maturities of marketable securities.

Net Cash provided by Financing Activities

For the nine months ended September 30, 2025, financing activities provided $21.5 million of cash, primarily related to the issuance and sale of 527,437 shares of common stock, net of paid issuance costs, pursuant to the ATM.

For the nine months ended September 30, 2024, financing activities provided $450.8 million of cash, primarily related to the issuance and sale of 7,790,321 shares of common stock, net of paid issuance costs, in our March 2024 Offering.

Future Funding Requirements

To date, we have not generated any revenue from product sales. We do not expect to generate revenue from product sales unless and until we successfully complete preclinical and clinical development of, receive regulatory approval for, and commercialize a product candidate and we do not know when that will occur, if at all. We expect our expenses to increase substantially in connection with our ongoing activities, particularly as we advance the preclinical and clinical activities. In addition, if we obtain regulatory approval for any product candidates, we expect to incur significant expenses related to product sales, marketing, and distribution to the extent that such sales, marketing and distribution are not the responsibility of potential collaborators. We expect to incur additional costs associated with operating as a public company. The timing and amount of our operating expenditures will depend largely on the factors set out above. For more information, see the section titled “Risk Factors—Risks Related to Our Limited Operating History, Financial Position and Capital Requirements.”

Our funding requirements and timing and amount of our operating expenditures will depend on many factors, including, but not limited to:

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the rate of progress in the development of our APG777, APG279, APG273, APG990, APG333 and APG808 programs;

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the scope, progress, results and costs of preclinical studies and clinical trials for any other current and future programs;

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the number and characteristics of programs and technologies that we develop or may in-license;

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the costs and timing of future commercialization activities, including manufacturing, marketing, sales and distribution, for any of our product candidates for which we receive marketing approval;

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the costs necessary to obtain regulatory approvals, if any, for any approved products in the United States and other jurisdictions, and the costs of post-marketing studies that could be required by regulatory authorities in jurisdictions where approval is obtained;

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the costs and timing of preparing, filing and prosecuting patent applications, maintaining and enforcing our intellectual property rights and defending any intellectual property-related claims, including claims of infringement, misappropriation or other violation of third-party intellectual property;

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the continuation of our existing licensing arrangements and entry into new collaborations and licensing arrangements;

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the costs we incur in maintaining business operations;

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the costs of hiring additional clinical, quality control, manufacturing and other scientific personnel;

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the costs of adding operational, financial and management information systems and personnel;

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adverse global macroeconomic conditions, including inflation, slower growth or recession, new or increased tariffs and other barriers to trade, changes to fiscal and monetary policy or government budget dynamics (particularly in the pharmaceutical and biotech areas), volatility in financial markets and other challenges in the global economy;

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the costs associated with being a public company;

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the costs and timing of future laboratory facilities;

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the revenue, if any, received from commercial sales of our product candidates for which we receive marketing approval;

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the effect of competing technological and market developments; and

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the extent to which we acquire or invest in businesses, products and technologies, including entering into licensing or collaboration arrangements for programs.

Identifying potential programs and product candidates and conducting preclinical studies and clinical trials is a time consuming, expensive and uncertain process that takes years to complete, and we may never generate the necessary data or results required to obtain marketing approval and achieve product sales. In addition, our product candidates, if approved, may not achieve commercial success. Our commercial revenues, if any, will be derived from sales of products that we do not expect to be commercially available for many years, if ever. Accordingly, we will need to obtain substantial additional funds to achieve our business objectives.

Adequate additional funds may not be available to us on acceptable terms, or at all. We do not currently have any committed external source of funds. To the extent that we raise additional capital through the sale of equity or convertible debt securities, our stockholders’ ownership interests could be diluted, and the terms of these securities may include liquidation or other preferences that could adversely affect our stockholders’ rights.

Additional debt financing and preferred equity financing, if available, may involve agreements that include covenants limiting or restricting our ability to take specific actions, such as incurring debt, making capital expenditures or declaring dividends, and may require the issuance of warrants, which could potentially dilute our stockholders’ ownership interests.

If we raise additional funds through strategic collaborations, licensing arrangements, royalty financings or other collaborations 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. Any additional fundraising efforts may divert our management from their day-to-day activities, which may adversely affect our business.

If we are unable to raise additional funds when needed or on acceptable terms, we may be required to delay, limit, suspend, or terminate our product development programs or any future commercialization efforts or grant rights to develop and market product candidates to third parties that we would otherwise prefer to develop and market ourselves.

As of September 30, 2025, we had $107.9 million of cash and cash equivalents, $419.4 million of marketable securities and $61.6 million of long-term marketable securities. Based on our current operating plan, as of the date of this Quarterly Report, we estimate that our existing cash, cash equivalents, marketable securities and long-term marketable securities will be sufficient to enable us to fund our operating expenses and capital expenditure requirements through at least the next 12 months following the issuance of our consolidated financial statements included elsewhere in this Quarterly Report. Moreover, based on our current operating plan, we estimate that such funds (including the $324.1 million in net proceeds from the October 2025 Offering) will be sufficient to enable us to fund our operating expenses and capital expenditure requirements into the second half of 2028. We have based this estimate on assumptions that may prove to be wrong, and we could exhaust our available capital resources sooner than we expect.

Contractual Obligations and Other Commitments

We enter into contracts in the normal course of business with contract research organizations (“CROs”), contract manufacturing organizations (“CMOs”) and other third parties for preclinical research studies and testing, clinical trials, manufacturing and other services. These contracts do not contain any minimum purchase commitments and provide for termination by us upon prior written notice. Payments due upon cancellation consist only of payments for services provided and expenses incurred up to the date of cancellation, including non-cancelable obligations of our service providers and, in some cases, wind-down costs. The exact amounts of such obligations are dependent on the timing of termination and the terms of the associated agreement. Accordingly, these payments are not disclosed as the amount and timing of such payments are not known.

Our agreements to license intellectual property include potential milestone payments that are dependent upon the development of products using the intellectual property licensed under the agreements and contingent upon the achievement of specific development and clinical milestones. As of September 30, 2025, we have incurred $17.0 million of the maximum aggregate potential milestone payments. We are also obligated to pay royalties to (i) Paragon at a royalty rate of a low single-digit percentage based on net sales of any products under the License Agreements, once commercialized and (ii) WuXi Biologics at a royalty rate of a fraction of a single digit percentage of global net sales of WuXi Biologics Licensed Products manufactured by a third-party manufacturer.

We do not have any off-balance sheet arrangements that are material or reasonably likely to become material to our financial condition or results of operations.

Critical Accounting Policies and Significant Judgments and Estimates

Our management’s discussion and analysis of our financial condition and results of operations is based on our consolidated financial statements, which have been prepared in accordance with generally accepted accounting principles in the United States. The preparation of these condensed consolidated financial statements requires us to make estimates and assumptions that affect the reported amounts of assets and liabilities and the disclosure of contingent assets and liabilities at the date of the condensed consolidated financial statements, as well as the reported revenues recognized and expenses incurred during the reporting periods. Our estimates are based on our historical experience and on various other factors that we believe are reasonable under the circumstances, the results of which form the basis for making judgments about the carrying value of assets and liabilities that are not readily apparent from other sources. Actual results may differ from these estimates under different assumptions or conditions.

We define our critical accounting policies as those accounting principles generally accepted in the United States of America that are most critical to the judgments and estimates used in the preparation of our condensed consolidated financial statements. While our significant accounting policies are described in more detail in Note 2 to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report, we believe that our most critical accounting policies are those relating to Research and Development

Expenses, which are described under the heading “Management’s Discussion and Analysis of Financial Condition and Results of Operations – Critical Accounting Policies and Significant Judgment and Estimates” in our Annual Report on Form 10-K. There have been no material changes to our critical accounting policies from those described in the Annual Report on Form 10-K.

Recently Issued Accounting Pronouncements

We have reviewed all recently issued accounting standards and have determined that, other than as disclosed in Note 2 to our condensed consolidated financial statements included elsewhere in this Quarterly Report, such standards are not expected to have a material impact on our consolidated financial statements or do not otherwise apply to our operations.