Stockholders’ Equity

9 Months Ended

Sep. 30, 2025

Equity [Abstract]

Stockholders’ Equity

Stockholders’ Equity

Common stock and pre-funded warrants

In March 2025, the Company’s board of directors approved the Neurogene Inc. 2025 Inducement Plan, which reserves for issuance up to 500,000 shares of the Company’s common stock underlying inducement awards.

In April 2025, the Company entered into an exchange agreement with existing stockholders to exchange an aggregate of 667,500 shares of the Company’s common stock for pre-funded warrants to purchase an aggregate of 667,563 shares of the Company’s common stock at an exercise price of $0.001 per share. The exchange was executed to facilitate the investor’s beneficial ownership thresholds. The exchange was accounted for as an equity-for-equity transaction. The Company derecognized the common shares and recognized an equivalent value in pre-funded warrants, with no gain or loss recognized.

In August 2025, the Company entered into an at-the-market (“ATM”) sales agreement (the “Sales Agreement”) with Leerink Partners, LLC (“Leerink”), as sales agents, pursuant to which the Company may offer and sell, from time to time, shares of the Company’s common stock with an aggregate price up to $150.0 million through Leerink.

In connection with the Sales Agreement, the Company incurred approximately $0.2 million of offering costs. These offering costs will be ratably recognized as a reduction to additional paid-in-capital as shares are sold under the Sales Agreement.

In September 2025, the Company received $9.8 million in net proceeds from the sale of 500,000 shares of the Company’s common stock pursuant to the Sales Agreement.

The Company has pre-funded warrants outstanding to purchase an aggregate of 6,792,559 shares of the Company’s common stock as of September 30, 2025. The pre-funded warrants are exercisable at any time for exercise prices ranging from $0.000001 to $0.001, except that the pre-funded warrants cannot be exercised by a holder if, after giving effect thereto, such holder would beneficially own more than 9.99% of the Company’s outstanding common stock, subject to certain exceptions. However, any holder may increase or decrease such percentage to any other percentage (not in excess of 19.99%) upon at least 61 days’ prior notice from the holder to the Company. The holders of the pre-funded warrants will not have the right to vote the shares underlying the pre-funded warrants on any matter except to the extent required by Delaware law. These warrants are classified as equity. Information on the outstanding warrants is as follows:

Type	Exercise Price		Amount	Type of Financing
Common stock pre-funded warrant	$	0.000001	425,987	Legacy pre-funded warrants outstanding
Common stock pre-funded warrant	$	0.000001	1,708,332	December 2023 preferred stock conversion
Common stock pre-funded warrant	$	0.000001	1,825,635	December 2023 Pre-Closing Financing
Common stock pre-funded warrant	$	0.001	2,165,042	November 2024 private placement
Common stock pre-funded warrant	$	0.001	667,563	April 2025 common stock conversion
Total			6,792,559

The Company has reserved shares of the Company’s common stock for future issuance as follows:

	September 30, 2025	December 31, 2024
Unvested restricted stock units	257,797	222,530
Unvested performance stock units	252,124	252,124
Options outstanding	2,112,391	1,387,556
Shares available for future grant under the 2023 Equity Incentive Plan	1,264,089	1,458,188
Shares available for future grant under the 2025 Inducement Plan	409,490	—
Shares available for future issuance under the 2023 Employee Stock Purchase Plan	321,770	173,223
Pre-funded warrants outstanding	6,792,559	6,124,996
Total common stock reserved	11,410,220	9,618,617