UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

Form 8-K

Current Report

Pursuant to Section 13 or 15(d)

of The Securities Exchange Act of 1934

Date of Report (Date of earliest event reported): May 22, 2015

MEDICINOVA, INC.

(Exact name of registrant as specified in its charter)

Registrant’s telephone number, including area code: (858) 373-1500

Not applicable.

(Former name or former address, if changed since last report.)

Check the appropriate box below if the Form 8-K filing is intended to simultaneously satisfy the filing obligation of the registrant under any of the following provisions (see General Instruction A.2. below):

On May 22, 2015, MediciNova, Inc. (the “Company”) entered into an at-the-market issuance sales agreement (the “sales agreement”) with MLV & Co. LLC (“MLV”), pursuant to which the Company may issue and sell shares of its common stock having an aggregate offering price of up to $30 million from time to time through MLV as the Company’s sales agent. The issuance and sale of these shares by the Company under the sales agreement, if any, is subject to the continued effectiveness of the Company’s shelf registration statement on Form S-3 (File No. 333-185022) declared effective by the Securities and Exchange Commission on December 3, 2012. The Company makes no assurance as to the continued effectiveness of its shelf registration statement.

Sales of the Company’s common stock through MLV, if any, will be made by any method that is deemed to be an “at-the-market” equity offering as defined in Rule 415 promulgated under the Securities Act of 1933, as amended, including sales made directly on The NASDAQ Stock Market (“NASDAQ”), on any other existing trading market for the common stock or to or through a market maker. MLV may also sell the common stock in privately negotiated transactions, subject to the Company’s prior approval.

Each time the Company wishes to issue and sell common stock under the sales agreement, the Company will provide a placement notice to MLV containing the parameters in accordance with which shares are to be sold, including, but not limited to, the number of shares to be issued and the dates on which such sales are requested to be made, subject to the terms and conditions of the sales agreement.

Subject to the terms and conditions of the sales agreement, MLV will use commercially reasonable efforts consistent with its normal trading and sales practices to sell the Company’s common stock from time to time, based upon the Company’s instructions (including any price, time or size limits the Company may impose pursuant to the terms of the sales agreement). The Company is not obligated to make any sales of common stock under the sales agreement and may terminate the sales agreement at any time upon written notice. The Company will pay MLV a commission of up to 4% of the gross proceeds from each sale. The Company has provided MLV with customary indemnification rights.

The foregoing description of the sales agreement is not complete and is qualified in its entirety by reference to the full text of such agreement, a copy of which is filed herewith as Exhibit 10.1 to this Current Report on Form 8-K and is incorporated herein by reference. This Current Report on Form 8-K also incorporates by reference the sales agreement into the Company’s above-referenced shelf registration statement on Form S-3.

This Current Report on Form 8-K shall not constitute an offer to sell or the solicitation of an offer to buy the securities discussed herein, nor shall there be any offer, solicitation, or sale of the securities in any jurisdiction in which such offer, solicitation or sale would be unlawful prior to registration or qualification under the securities laws of any such jurisdiction.

In connection with entering into the new at-the-market offering program as described in Item 1.01 above, on May 22, 2015, the Company gave notice to Macquarie Capital (USA) Inc. (“MCUSA”) that the Company had elected to terminate the equity distribution agreement dated October 16, 2013 by and between the Company and MCUSA, thereby terminating the Company’s existing at-the-market offering program and the related public offering of the Company’s common stock made pursuant to the Prospectus Supplement dated October 16, 2013.

(d) Exhibits.

SIGNATURE

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned hereunto duly authorized.

EXHIBIT INDEX