SECURITIES AND EXCHANGE COMMISSION

Washington, DC 20549

SCHEDULE 13G/A

(Rule 13d-102)

(Amendment No. 1)

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(b)

KAYAK Software Corporation

(Name of Issuer)

Class A Common Stock, $0.001 par value

(Title of Class of Securities)

486577109

(CUSIP Number)

January 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:

x Rule 13d-1(b)

¨ Rule 13d-1(c)

¨ Rule 13d-1(d)

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SCHEDULE 13G/A

This Amendment No. 1 (this “Amendment”) to the Schedule 13G (the “Schedule 13G”) relates to shares of Class A Common Stock, par value $0.001 per share (the “Common Stock”), of KAYAK Software Corporation, a Delaware corporation (the “Issuer”), and is being filed on behalf of (i) of Nokota Management LP, a Delaware limited partnership (“Nokota Management”), as the investment manager to certain private investment funds (the “Funds”), (ii) Nokota Advisors, LLC, a Delaware limited liability company (“Nokota Advisors”), as the general partner of Nokota Management, (iii) Matthew Knauer, an individual, as a manager of Nokota Advisors, and (iv) Mina Faltas, an individual, as a manager of Nokota Advisors (the persons mentioned in (i) (ii), (iii) and (iv) above are referred to as the “Reporting Persons”). All shares of Common Stock reported in this Amendment are held by the Funds.

This Amendment amends and restates the Schedule 13G as set forth below.

KAYAK Software Corporation

55 North Water Street, Suite 1

Norwalk, CT 06854

(a)  Nokota Management LP (“Nokota Management”);

(b)  Nokota Advisors, LLC (“Nokota Advisors”);

(c)  Matthew Knauer; and

(d)  Mina Faltas

1330 Avenue of the Americas

26th Floor

New York, NY 10019

Nokota Management is a limited partnership organized under the laws of the State of Delaware. Nokota Advisors is a limited liability company organized under the laws of the State of Delaware. Matthew Knauer and Mina Faltas are United States citizens.

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Shares of Class A Common Stock, par value $0.001 per share (the “Common Stock”).

486577109

If this statement is filed pursuant to Rule 13d-1(b), or 13d-2(b), check whether the person filing is a:

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Inapplicable.

Inapplicable.

Inapplicable.

Inapplicable.

Inapplicable.

By signing below each of the Reporting Persons certifies that, to the best of such person’s knowledge and belief, the securities referred to above were acquired and held in the ordinary course of business and were not acquired and were not held for the purpose of or with the effect of changing or influencing the control of the issuer of the securities and were not acquired and are not held in connection with or as a participant in any transaction having that purpose or effect.

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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: February 27, 2013

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