UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No. 3)*

FLOW INTERNATIONAL CORPORATION

(Name of Issuer)

COMMON STOCK, PAR VALUE $0.01

(Title of Class of Securities)

343468104

(CUSIP Number)

John G. Igoe, P.A.

Edwards Wildman Palmer LLP

525 Okeechobee Boulevard, Suite 1600

West Palm Beach, Florida 33401

(561) 833-7700

(Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications)

April 9, 2013

(Date of Event Which Requires Filing This Statement)

If the filing person has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of §§240.13d-1(e), 240.13d-1(f) or 240.13d-1(g), check the following box.  ¨

NOTE: Schedules filed in paper format shall include a signed original and five copies of the schedule, including all exhibits. See §240.13d-7 for other parties to whom copies are to be sent.

The information required on the remainder of this cover page shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934 (“Exchange Act”) or otherwise subject to the liabilities of that section of the Exchange Act but shall be subject to all other provisions of the Exchange Act (however, see the Notes).

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This Amendment No. 3 to Schedule 13D amends the Schedule 13D filed on August 12, 2011, as amended March 21, 2012 and March 27, 2013 (the “Original Statement”, and as amended by this Amendment No. 3, this “Schedule 13D”) and is being filed pursuant to Rule 13d-2(a) under the Securities Exchange Act of 1934, as amended (the “Exchange Act”), on behalf of Otter Creek Partners I, L.P., a Delaware limited partnership (the “Domestic Fund”), Otter Creek International, Ltd., a British Virgin Islands international business company (the “Offshore Fund”), Otter Creek Management, Inc., a Delaware corporation (the “Management Company”) and R. Keith Long, an individual (“Mr. Long” and, together with the Domestic Fund, the Offshore Fund and the Management Company, the “Reporting Persons”).

This Schedule 13D relates to the common stock, par value $0.01 per share, of Flow International Corporation, a Washington corporation (the “Issuer”), which has principal executive offices located at 23500 64th Avenue South, Kent, Washington 98032. Unless the context otherwise requires, references herein to the “Common Stock” are to such Common Stock of the Issuer. The Management Company is the sole general partner of the Domestic Fund and the investment adviser to the Domestic Fund and the Offshore Fund (collectively, the “Funds”). The Funds directly own the Common Stock to which this Schedule 13D relates, and the Reporting Persons may be deemed to have beneficial ownership over such Common Stock by virtue of the authority granted to them by the Funds to vote and to dispose of the securities held by the Funds, including the Common Stock.

Item 4. Purpose of Transaction.

Item 4 of the Original Statement is hereby supplemented as follows: On April 9, 2013, the Funds submitted a shareholder proposal pursuant to Rule 14a-8 of the Securities Exchange Act of 1934, as amended, for inclusion in the Issuer’s proxy statement for its 2013 annual meeting of shareholders, requesting that the Issuer promptly take action to de-classify its Board of Directors. A copy of the submission is filed as Exhibit 99.3 to this Schedule 13D.

Item 5. Interest in Securities of the Issuer.

Item 5 of the Original Statement is hereby amended and restated in its entirety as follows:

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Transactions by the Domestic Fund

Transactions by the Offshore Fund

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Item 7. Material to Be Filed as Exhibits.

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SIGNATURES

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.

Dated: April 15, 2013

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Exhibit 99.3

OTTER CREEK MANAGEMENT, INC.

222 LAKEVIEW AVENUE

SUITE 1100

WEST PALM BEACH, FLORIDA 33401

561-832-4110

FAX 561-655-6902

Email: KLONG@OTTERCREEKMGT.COM

SHAREHOLDER-BOARD COMMUNICATION

April  9^th, 2013

John S. Leness

Corporate Secretary

Flow International Corporation

23500 64^th Avenue South

Kent, WA 98032

Dear Mr. Leness:

Please be advised that Otter Creek Management, Inc., on behalf of Otter Creek Partners I, L.P. and Otter Creek International, Ltd., hereby submits the enclosed shareholder resolution to be presented at the 2013 annual meeting of Flow International Corporation (the “Company”), pursuant to Rule 14a-8 promulgated under the Securities Exchange Act of 1934. Otter Creek Management, Inc. is the sole general partner of Otter Creek Partners I, L.P. and the investment advisor to Otter Creek Partners I, L.P. and Otter Creek International, Ltd.

As of April 9^th, 2013, Otter Creek Partners I, L.P., with a business address of 222 Lakeview Avenue, Suite 1100, West Palm Beach, FL 33401, is the beneficial owner of 1,081,703 shares of Common Stock of the Company. Otter Creek Partners I, L.P. has owned shares of the Company’s Common Stock valued at $2,000 for a period in excess of one year prior to this submission. Otter Creek Partners I, L.P. intends to hold the number of shares required to submit shareholder resolutions through the date of the Company’s 2013 annual meeting.

As of April 9^th, 2013, Otter Creek International, Ltd., with a business address of 222 Lakeview Avenue, Suite 1100, West Palm Beach, FL 33401, is the beneficial owner of 1,507,713 shares of Common Stock of the Company. Otter Creek International, Ltd. has owned shares of the Company’s Common Stock valued at $2,000 for a period in excess of one year prior to this submission. Otter Creek International, ltd. intends to hold the number of shares required to submit shareholder resolutions through the date of the Company’s 2013 annual meeting.

Enclosed herewith are the shareholder proposal and supporting statement, along with Appendix A showing verification of ownership of the shares of the Company’s Common Stock referenced above as contemplated by Rule 14a-8(b)(2)(ii), in the form of the Schedule 13D dated August 12, 2011 and all amendments thereto filed by and on behalf of the undersigned regarding ownership of Common Stock of the Company.

Please acknowledge receipt of this proposal promptly by emailing me at KLONG@OTTERCREEKMGT.COM and do not hesitate to contact me with any questions you may have.

Sincerely,

PROPOSAL TO REPEAL CLASSIFIED BOARD

RESOLVED, that shareholders of Flow International Corporation urge the Board of Directors to take the steps necessary (other than any steps that must be taken by shareholders) to eliminate the classification of the Board of Directors and to require that all directors elected at or after the annual meeting held in 2014 be elected on an annual basis. Implementation of this proposal should not prevent any director elected prior to the annual meeting held in 2014 from completing the term for which such director was elected.

SUPPORTING STATEMENT

We urge the Flow Board of Directors to bring the Flow board election process up to present state of the art good governance standards by eliminating staggered board elections. Over the past decade many companies have declassified their board of directors. According to the Shareholder Rights Project at Harvard Law School, in 2012 alone fully one-third of the S&P 500 companies with a staggered board at the beginning of the year declassified during the year.

The significant shareholder support for declassification proposals is consistent with empirical studies reporting that:

Although one study (Bates, Becher and Lemmon, 2008) reports that classified boards are associated with higher takeover premiums, this study also reports that classified boards are associated with a lower likelihood of an acquisition and that classified boards are associated with lower firm valuation.

Flow International has underperformed for decades. Shareholders deserve the right to elect a full slate of directors who will be accountable to shareholders and will act in their best interest.

Appendix A

Verification of Ownership of Shares of Common Stock of

Flow International Corporation

Enclosed: