SECURITIES AND EXCHANGE COMMISSION

Washington, DC 20549

SCHEDULE 13G/A

(Rule 13d-102)

INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO

RULES 13d-1(b), (c) AND (d) AND AMENDMENTS THERETO FILED

PURSUANT TO RULE 13d-2

UNDER THE SECURITIES EXCHANGE ACT OF 1934

(Amendment No. 3)

Geeknet, Inc.

(Name of Issuer)

Common Stock, par value $0.001 per share

(Title of Class of Securities)

36846Q203

(CUSIP Number)

December 31, 2013

(Date of Event Which Requires Filing of this Statement)

Check the appropriate box to designate the rule pursuant to which this Schedule is filed:

¨ Rule 13d-1(b)

x Rule 13d-1(c)

¨ Rule 13d-1(d)

SCHEDULE 13G

This Amendment No. 3 to Schedule 13G (this “Amendment”) is being filed on behalf of TCS Global Equity Master Fund, L.P., a Cayman Islands exempted limited partnership (“TCS Global”), TCS Capital GP, LLC, a Delaware limited liability company (“TCS GP”), and TCS Capital Management, LLC, a Delaware limited liability company (“TCS Management” and, together with TCS Global and TCS GP, the “Reporting Persons”). This Amendment relates to common stock, par value $0.001 per share (the “Common Stock”) of Geeknet, Inc., a Delaware corporation (the “Issuer”). TCS GP acts as general partner to TCS Global and TCS Management acts as investment manager to TCS Global.

This Amendment serves as an amendment to the Schedule 13G originally filed on February 28, 2011 and amended February 14, 2012 and February 14, 2013 (the “Schedule 13G”) and is being filed to report that the Reporting Persons no longer own shares of Common Stock of the Issuer. Eric Semler, who was previously included as a reporting person on the Schedule 13G, will now file separately in his individual capacity. This Amendment amends and restates the below items as follows.

SIGNATURE

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

Date: January 23, 2015

EXHIBIT 99-1

JOINT FILING AGREEMENT

In accordance with Rule 13d-1(k) under the Securities Exchange Act of 1934, as amended, the undersigned agree to the joint filing on behalf of each of them of a Statement on Schedule 13G (including any and all amendments thereto) with respect to the securities of Geeknet, Inc., and further agree that this Joint Filing Agreement shall be included as an Exhibit to such joint filings.

The undersigned further agree that each party hereto is responsible for the timely filing of such Statement on Schedule 13G and any amendments thereto, and for the accuracy and completeness of the information concerning such party contained therein; provided, however, that no party is responsible for the accuracy or completeness of the information concerning any other party, unless such party knows or has reason to believe that such information is inaccurate.

This Joint Filing Agreement may be signed in counterparts with the same effect as if the signature on each counterpart were upon the same instrument.

IN WITNESS WHEREOF, the undersigned have executed this Agreement as of January 23, 2015.