Septerna, Inc. Stock Compensation Disclosure

10. Stock-Based Compensation

2024 Stock Option and Incentive Plan

In October 2024, the Company's board of directors adopted, and its stockholders approved, the 2024 Stock Option and Incentive Plan (the “2024 Plan”) which became effective on October 25, 2024. The 2024 Plan allows for the issuance of equity-based incentive awards to the Company's officers, employees, directors and consultants.

The 2024 Plan provides that the number of shares reserved and available for issuance under the 2024 Plan will automatically increase on January 1, 2025 and each January 1 thereafter through January 1, 2034 by 5% of the outstanding number of shares of the Company's common stock on the immediately preceding December 31 or such lesser number of shares as determined by the Company's compensation committee.

The 2024 Plan replaced the Septerna, Inc. 2021 Stock Option and Grant Plan (the “2021 Plan”) as the Company’s board of directors determined not to make additional awards under the 2021 Plan following the completion of the IPO. However, the 2021 Plan will continue to govern outstanding equity awards granted thereunder. The shares of common stock underlying any awards under the 2024 Plan and the 2021 Plan that are forfeited, cancelled, held back upon exercise or settlement of an award to satisfy the exercise price or tax withholding, reacquired by the Company prior to vesting, satisfied without the issuance of stock, expire or are otherwise terminated (other than by exercise) will be added to the shares of the Company's common stock available for issuance under the 2024 Plan. 4.3 million and 3.7 million shares remained available for future issuance under the 2024 Plan as of December 31, 2025 and 2024, respectively.

Stock options are governed by stock option agreements between the Company and recipients of stock options. Incentive stock options and nonqualified stock options may be granted under the 2024 Plan at an exercise price of not less than 100% of the fair market value of the common stock on the date of grant, determined by the Compensation Committee of the board of directors. Options become exercisable and expire as determined by the Compensation Committee, provided that the term of the stock options may not exceed ten years from the date of grant.

2021 Stock Option and Grant Plan

In 2021, the Company adopted the 2021 Plan, which authorizes the Company to grant incentive stock options, non-qualified stock options, restricted stock awards, unrestricted stock awards and restricted stock units, to officers, employees, directors, consultants, or other key persons of the Company. The terms of the stock option and restricted stock agreements, including vesting requirements, are determined by the Board of Directors, subject to the provisions of the 2021 Plan. Stock option awards expire 10 years from the grant date, or as otherwise determined by the Board of Directors, or in the case of incentive stock options granted to 10% stockholders, the term is no more than 5 years from the grant date. Additionally, the Company granted and issued restricted stock awards and allowed the recipients to purchase the unvested restricted stock awards at par value per share. The shares issued for unvested restricted stock awards under the 2021 Plan are subject to repurchase by the Company at the original issuance price in the event of the holder’s termination of its relationship with the Company. Consideration received for shares associated with the unvested restricted stock awards is initially recorded as a liability and subsequently reclassified into stockholders’ equity as the related awards vest over the requisite service period.

No shares remained available for future issuance under the 2021 Plan as of December 31, 2025 and 2024 as the 2021 Plan was replaced by the 2024 Plan.

Restricted Stock Awards

The Company granted restricted stock awards from the 2021 Plan and from outside of its stock plans, under the terms of restricted stock purchase agreements and subscription agreements. Unvested shares are subject to repurchase by the Company upon the holder’s termination of its relationship with the Company at the original purchase price. Consideration received for shares associated with the

unvested restricted stock awards is initially recorded as a liability and subsequently reclassified into stockholders’ equity as the related awards vest.

The restricted stock awards generally include a service condition for vesting and vest over four years with a one-year cliff vesting and pro-rata monthly vesting thereafter, but some awards vest over different time periods. In addition, some restricted stock awards include vesting criteria subject to the achievement of performance-based conditions in addition to service conditions (“performance RSAs”). As of December 31, 2025, none of the outstanding and unvested performance RSAs were subject to achievement of performance-based criteria for vesting. The aggregate grant date fair value of shares vested during the year ended December 31, 2025 was $1.3 million. The remaining liability related to restricted stock awards as of December 31, 2025 was not material and was recorded in accrued expenses and other current liabilities on the balance sheet.

Stock Options

Stock options include a service condition for vesting and generally vest over four years. The aggregate intrinsic values of options outstanding and exercisable were calculated as the difference between the exercise price of the options and the closing market price of the Company’s common stock as of December 31, 2025.

The aggregate grant date fair value of options that vested for the year ended December 31, 2025 was $4.9 million. The options granted in the year ended December 31, 2025 and 2024 had a weighted-average per share grant-date fair value of $9.58 and $6.65, respectively, and a total grant date fair value of $18.3 million and $13.1 million, respectively. The total intrinsic value of stock options exercised during the year ended December 31, 2025 was $2.2 million.

2024 Employee Stock Purchase Plan

In October 2024, the Company's board of directors adopted, and its stockholders approved, the 2024 ESPP. The 2024 ESPP provides that the number of shares reserved and available for issuance will automatically increase on January 1, 2026 and each January 1 thereafter through January 1, 2034, by the lesser of (i) 0.4 million shares of common stock, (ii) 1% of the outstanding number of shares

of common stock on the immediately preceding December 31, or (iii) such lesser number of shares of common stock as determined by the administrator of the 2024 ESPP.

The 2024 ESPP provides eligible employees with an opportunity to purchase common stock from the Company and to pay for their purchases through payroll deductions.

The offering periods begin on May 1 and November 1, will be twenty-four (24) months in duration and include four (4) purchase periods, each purchase period lasting six (6) months. The purchase price will be 85% of the fair market value per share of the Company's common stock on either the offering date, which is the first trading day of the offering period, or the purchase date, which is the last trading day of the purchase period, whichever is less. If the fair market value of a share of the Company's common stock on any purchase date within a particular offering period is less than the fair market value on the start date of that offering period, then the offering period will automatically terminate and the employees in that offering period will automatically be transferred and enrolled in a new offering period which will begin on the next day following such purchase date.

During the year ended December 31, 2025, the Company issued 118,191 shares at a weighted average share price of $6.07 per share. As of December 31, 2025, there were 0.3 million shares available for issuance under the 2024 ESPP.

Stock Option and ESPP Valuation

In determining the fair value of the stock options and ESPP granted, the Company uses the Black-Scholes option pricing model and assumptions discussed below. This model utilizes inputs that are subjective.

Expected Term — The expected term represents the period that the Company’s stock options granted are expected to be outstanding and is determined using the simplified method (based on the mid-point between the vesting date and the end of the contractual term). The Company has very limited historical information to develop reasonable expectations about future exercise patterns and post-vesting employment termination behavior for its stock option grants. The Company will continue to apply this process until a sufficient amount of historical information regarding employee exercise patterns and post-vesting employment termination behavior becomes available.

Expected Volatility — Due to the Company’s limited operating history and lack of company-specific historical volatility as a public company, due to the Company's IPO in October 2024, or implied volatility as a private company, the expected volatility was estimated based on the average volatility for comparable publicly traded biopharmaceutical companies over a period, where available, equal to the expected term of the stock option grants. The comparable companies were chosen based on their similar size, life cycle stage and area of specialty.

Risk-free Interest Rate — The risk-free interest rate is based on the U.S. Treasury zero coupon issues in effect at the time of grant for periods corresponding with the expected term of the options.

Expected Dividend — The Company has never paid dividends on its common stock and does not anticipate paying dividends on its common stock in the near future. Therefore, the Company used an expected dividend yield of zero.

Stock-based Compensation Expense

As of December 31, 2025, total unrecognized stock-based compensation expense related to unvested restricted stock awards, stock options, and ESPP was $24.5 million, which is expected to be recognized over a weighted-average period of 2.7 years.