Apellis Pharmaceuticals, Inc. Stock Compensation Disclosure

14. Equity Incentive Plans

Share-based Compensation

The Company’s Board of Directors adopted, and its stockholders approved, an equity incentive plan in 2010 (as amended, the “2010 Plan”). The Board of Directors and stockholders amended the 2010 Plan in August 2017 to increase the number of shares of common stock reserved for issuance thereunder to 6,188,466. The 2010 Plan allowed for the grant of incentive stock options and non-qualified stock options to purchase common stock for employees, directors and consultants under terms and conditions established by the Board of Directors. Incentive stock options and nonqualified stock options were granted at exercise prices that were no less than 100% of the estimated fair value per share of the common stock on the date of grant. If an individual owns capital stock representing more than 10% of the voting shares, the price of each share was at least 110% of the fair value on the date of grant. The Board of Directors determined the fair value of common stock with the assistance of a third-party specialist. Options expire 10 years from the issuance date. Following the adoption of Company’s the 2017 Stock Incentive Plan (the “2017 Plan”), the Company no longer grants stock options or other awards under the 2010 Plan.

In October 2017, the Company’s Board of Directors adopted, and its stockholders approved, the 2017 Plan, which became effective on November 8, 2017. The 2017 Plan provides for the grant of incentive stock options, non-statutory stock options, stock appreciation rights, awards of restricted stock, restricted stock units and other stock-based awards. The number of shares of common stock reserved for issuance under the 2017 plan is the sum of (i) 1,359,587 shares of common stock, plus (ii) an additional number of shares of common stock equal to the sum of (a) the number of shares of common stock reserved for issuance under the 2010 equity incentive plan that remained available for future issuance immediately prior to the effectiveness of the 2017 Plan, which was 299,568 shares, and (b) the number of shares of common stock subject to outstanding awards under the 2010 equity incentive plan upon effectiveness of the 2017 plan that expire, terminate or are otherwise surrendered, cancelled, forfeited or repurchased by us at their original issuance price pursuant to a contractual repurchase right plus (iii) an annual increase, to be added the first day of each fiscal year, beginning with the fiscal year ending December 31, 2018 and continuing until, and including, the fiscal year ending December 31, 2027, equal to the lowest of (i) 4,219,409 shares of common stock, (ii) 4.0% of the number of shares of common stock outstanding on the first day of the fiscal year and (iii) an amount determined by the board of directors. On January 1, 2025, the shares available for future issuance under the 2017 plan were increased by 4,219,409 shares pursuant to the annual increase described above. As of December 31, 2025, there were 2,865,381 shares available for future grants under the 2017 Plan. In January 2026, the shares available for future issuance under the 2017 plan were increased by an additional 4,219,409 shares.

Additionally, since 2019, the Company has granted equity awards as equity inducement awards material to entry into employment with the Company to certain newly hired employees outside of the Company’s existing plans in accordance with Nasdaq listing rule 5635(c)(4). In February 2020, the Board of Directors adopted the 2020 Inducement Stock Incentive Plan (the “2020 Plan”), which permitted the Company to grant equity awards to newly hired employees in accordance with Nasdaq listing rule 5635(c)(4).

The aggregate number of shares reserved for issuance under the 2020 Plan was initially 750,000 shares. The Board of Directors amended the 2020 Plan to add 200,000 shares on January 1, 2024, which increased the total number of shares reserved for issuance to 1,950,000 shares as of January 1, 2024. As of December 31, 2025, there were 1,032,021 shares available for future grants under the 2020 Plan. No additional shares have been reserved under the 2020 Plan in 2025 or 2026.

In October 2017, the Company’s board of directors adopted, and the Company’s stockholders approved the 2017 Employee Stock Purchase Plan (“ESPP”) and provides participating employees with the opportunity to purchase up to an aggregate of 468,823 shares of common stock. The number of shares of common stock reserved for issuance under the 2017 ESPP will automatically increase on the first day of each fiscal year, beginning with the fiscal year ending December 31, 2018 and continuing until, and including, the fiscal year ending December 31, 2027, equal to the lowest of (i) 937,646 shares of common stock, (ii) 1.0% of the number of shares of common stock outstanding on the first day of the fiscal year and (iii) an amount determined by the board of directors. The board of directors initiated the first offering under ESPP in October 2019. On December 31, 2025, 208,848 shares of common stock remained available for issuance pursuant to the ESPP. On January 1, 2026, the shares available for future issuance under the ESPP were increased by 500,000 shares pursuant to the annual increase described above.

Stock Options—Options granted to employees typically vest over 48 months in installments of (i) 25% at the one-year anniversary and (ii) in either 36 equal monthly or 12 equal quarterly installments beginning in the thirteenth month after the initial vesting commencement date (as defined) subject to the employee’s continuous service with the Company.

Under the Executive Separation Benefits and Retention Plan and by resolutions adopted by the Compensation Committee in October 2019, the stock options granted to the Company’s executives and employees will become fully vested upon the occurrence of a change in control, as defined in the Executive Separation Benefits and Retention Plan, if such executive or senior employee is terminated without cause or resigns for good reason within 12 months after such change in control.

The aggregate intrinsic values were calculated as the difference between the exercise price of the options and the fair value of the common stock.

During the years ended December 31, 2025, 2024 and 2023, the Company granted stock options to purchase an aggregate of 2.9 million, 0.7 million and 0.8 million shares of its common stock, respectively with weighted average grant date fair values per share of $9.66, $42.61 and $34.26, respectively.

The aggregate intrinsic value of options exercised during the years ended December 31, 2025, 2024 and 2023 were $3.0 million, $46.0 million, and $181.0 million, respectively, calculated as the difference between the exercise price of the options and the fair value of the common stock on the respective date of exercise.

As of December 31, 2025, unrecognized compensation expense related to unvested options was $32.3 million, which the Company expects to recognize over an estimated weighted-average period of 1.9 years.

Restricted Stock Units— The fair value of RSUs is estimated based upon the closing market price of the Company’s common stock on the date of grant. RSUs generally vest annually over a four-year period.

The fair value of restricted stock units vested during the year ended December 31, 2025, 2024 and 2023, respectively, were $74.6 million, $65.5 million and $42.2 million.

As of December 31, 2025, there was approximately $118.2 million of related unrecognized compensation cost which the Company expects to recognize over a remaining weighted average period of 2.5 years.

Performance and Market-Based Stock Unit Awards

Market-Based RSUs

In January 2025, the Company granted 646,488 shares of performance restricted stock units (“PSUs”) to each of its executives pursuant to the 2017 Plan. Each performance restricted stock unit represents a contingent right to receive one share of the Company’s common stock. The PSUs will vest, subject to the satisfaction of the market conditions outlined below, so long as the grantee has a continuing service relationship with the Company. All vesting is dependent on grantee remaining employed by the Company on the applicable vesting dates. The market condition shall mean the attainment of Company relative total shareholder return (“rTSR”) performance compared to the Nasdaq Biotechnology Index (“NBI”) during the following three performance periods: 2025, 2025 - 2026, and 2025 - 2027, as determined by the Compensation Committee of the board of directors, utilizing a twenty (20) business day average stock price preceding the commencement date and preceding the conclusion of the performance period, with the following potential target threshold payout:

• 25th percentile relative TSR = 50% of original number of rTSR PSUs

• 55th percentile relative TSR = 100% of the original number of rTSR PSUs

• 90th percentile or greater relative TSR = 200% of the original number of rTSR PSUs

The Company used a Monte Carlo model to estimate the grant-date fair value of the rTSR PSUs. Share-based compensation expense for the rTSR PSUs is recorded in the consolidated statement of operations and comprehensive income/(loss) over the service period regardless of whether the market condition is achieved. Assumptions and estimates utilized in the calculation of the fair value of the rTSR PSUs include the risk-free interest rate, dividend yield, expected volatility based on the historical volatility of the Company and the performance period of the award.

As of December 31, 2025, there was approximately $10.7 million of related unrecognized compensation cost which the Company expects to recognize over a remaining weighted average period of 1.6 years.

Performance-Based RSUs

In June 2025, the Company granted 1,238,937 performance-based RSUs to all active employees pursuant to the 2017 Plan. Each performance-based restricted stock unit represents a contingent right to receive one share of the Company’s common stock. The performance-based RSUs will vest, subject to the satisfaction of certain regulatory and revenue performance conditions, so long as the grantee has a continuing service relationship. The fair value of the performance-based RSUs is estimated based upon the closing market price of the Company’s common stock on the date of grant. Of the 1,238,937 performance-based RSUs legally granted, the Company notes a grant date per ASC Topic 718, Compensation – stock compensation (“ASC 718”) was only established for 743,265 awards as certain criteria to establish a grant date under ASC 718 was not met for 495,672 awards.

During the year ended December 31, 2025, no expense was recognized because the performance conditions were not considered probable of achievement.

Employee Stock Purchase Plan— Eligible employees who elect to participate in an offering under the ESPP may have up to 15% of their earnings withheld, subject to certain limitations, to purchase shares of common stock pursuant to the ESPP. The price of common stock purchased under the ESPP is equal to 85% of the lower of the fair market value of the common stock at the commencement date of each offering period or the relevant purchase date. During the year ended December 31, 2025, a total of 202,092 shares of common stock were issued under the ESPP at an average per share price of $16.58. During the year ended

December 31, 2025, the Company recorded cash received from the issuance of stock to the ESPP of $3.4 million and recorded $1.4 million of share-based compensation expense related to the ESPP.