7. Stock-Based Compensation

2025 Inducement Plan

On March 25, 2025, the Company’s board of directors adopted the RAPT Therapeutics, Inc. Inducement Plan (“2025 Inducement Plan”) and reserved 62,500 shares of its common stock to be used exclusively for grants of awards to individuals that were not previously employees or directors of the Company as a material inducement to such individuals’ entry into employment with the Company within the meaning of Rule 5635(c)(4) of the Nasdaq Listing Rules. As of June 30, 2025, no awards had been granted under the 2025 Inducement Plan.

2025 Equity Incentive Plan

The 2025 Equity Incentive Plan (the “2025 Plan”) was adopted by the Company’s board of directors on March 25, 2025 and approved by the Company’s stockholders at the 2025 Annual Meeting on May 29, 2025 (the “2025 Plan Effective Date”). The terms of the 2025 Plan provide for the grant of incentive stock options, nonstatutory stock options, stock appreciation rights, restricted stock awards, restricted stock unit awards, other stock awards, and performance awards that may be settled in cash, stock, or other property. Stock options may be granted under the 2025 Plan with an exercise price not less than 100% of the fair market value of the common stock on the date of grant. Stock options under the 2025 Plan may be granted with terms of up to ten years and generally vest over a period of four years, with the exception of grants to non-employee directors and consultants where the vesting period is or may be shorter. The total number of shares of the Company’s common stock initially reserved for issuance under the 2025 Plan was equal to the sum of 4,408,997 shares of common stock under the 2025 Plan, consisting of (i) 2,687,500 new shares of common stock reserved for issuance under the 2025 Plan, (ii) 196,798 shares of common stock that remained available for grant under the Company’s 2019 Equity Incentive Plan (the “2019 Plan”) as of the 2025 Plan Effective Date, which shares were rolled over into the 2025 Plan under the terms thereof and (iii) up to 1,524,699 shares of common stock subject to outstanding equity awards under the 2019 Plan and the Company’s 2015 Stock Plan (the “2015 Plan”) that, on or after the 2025 Plan Effective Date, may terminate, expire or lapse for any reason without the delivery of shares of common stock to the holder thereof and may potentially be returned due to forfeiture of such prior awards and, as a result, may become available for issuance under the 2025 Plan under the terms thereof. No new awards will be granted under the 2019 Plan on or after the 2025 Plan Effective Date and all outstanding awards previously granted under the 2019 Plan or 2015 Plan will remain outstanding, subject to the terms thereof.

As of June 30, 2025, 1,017,658 shares remained available for issuance under the 2025 Plan.

Amended and Restated 2019 Employee Stock Purchase Plan (as amended and restated, the “Amended ESPP”)

The Company's board of directors adopted the Amended and Restated 2019 Employee Stock Purchase Plan (as amended and restated, the “Amended ESPP”) on March 25, 2025, which was approved by the Company’s stockholders at the 2025 Annual Meeting. The Company’s Amended ESPP removed its evergreen provision and reserved an additional 500,000 shares of common stock for issuance.

Stock-based compensation expense

As of June 30, 2025, unrecognized stock-based compensation expense related to outstanding unvested stock options and RSUs that are expected to vest was $41.1 million. This unrecognized stock-based compensation expense is expected to be recognized over 2.8 years.

The Company recorded stock-based compensation expense related to the Amended ESPP of $0.3 million and $0.4 million for the three months ended June 30, 2025 and 2024, respectively, and $0.6 million and $0.7 million for the six months ended June 30, 2025 and 2024, respectively.

Repricing of stock options

On November 12, 2024, the compensation committee of the board of directors approved an option repricing, effective November 13, 2024 (the “Repricing Effective Date”). The repricing generally applied to options to purchase shares of the Company’s common stock that: (i) were granted under the 2019 Plan; (ii) as of the Repricing Effective Date, were held by the Company’s then-current employees and consultants (subject to the caveat below) (each, an “Eligible Participant”); and (iii) had an exercise price per share greater than $64.00 (the “Eligible Options”). The Eligible Options include options held by certain of the Company's executive officers. Options held by non-employee members of the Board were not eligible for the repricing program.

As of the Repricing Effective Date, the exercise price per share of the Eligible Options was reduced, subject to certain retention requirements outlined below, to the closing price per share of the Company’s common stock on the Repricing Effective Date, which was $12.56. If an employee exercises Eligible Options in advance of the end of the retention period as described below, the employee will be required to pay a premium exercise price equal to the original exercise price per share of the Eligible Options. There were no changes to the number of shares underlying the Eligible Options or to the vesting schedules or expiration dates of the Eligible Options.

In order to exercise the Eligible Options at the reduced exercise price, holders of the Eligible Options are required to remain in service with the Company through the end of the relevant retention period. The retention period begins on the Repricing Effective Date and ends on the earliest of the following: (i) the date 12 months following the Repricing Effective Date; (ii) a Change in Control (as defined in the 2019 Plan) if the Eligible Options are not assumed or continued by the successor or acquiror entity (or its parent company) in such Change in Control or substituted for a similar award of the successor or acquiror entity (or its parent company); or (iii) the option holder’s termination of Continuous Service (as defined in the 2019 Plan) (a) due to such individual’s death or disability, (b) by the Company (or successor entity in a Change in Control) other than for Cause (as defined in the applicable 2019 Plan) or (c) due to such option holder’s resignation on or following a Change in Control under certain circumstances.

As of the Repricing Effective Date, the total number of shares underlying the Eligible Options was 0.5 million shares. The effect of the repricing resulted in total incremental stock-based compensation expense of $1.6 million, $0.5 million of which will be recognized on a straight-line basis through the end of the retention period, while the remaining $1.1 million will be recognized on a straight-line basis over the original vesting period for those options that vest after the end of the retention period. The incremental stock-based compensation expense was calculated using the Monte Carlo option-pricing model.

For the three and six months ended June 30, 2025, the Company recognized incremental stock-based compensation expense totaling $0.2 million and $0.5 million, respectively, associated with the option repricing, which is included in general and administrative and research and development expense on the statement of operations.