<PAGE>

Exhibit 31.1

    CERTIFICATION OF BRIAN W. BENDER, SENIOR VICE PRESIDENT, CHIEF FINANCIAL
   OFFICER, CO-CHIEF EXECUTIVE OFFICER*, PURSUANT TO RULE 13a-14(a) UNDER THE
                   SECURITIES EXCHANGE ACT OF 1934, AS AMENDED

I, Brian W. Bender, certify that:

1. I have reviewed this quarterly report on Form 10-Q of ShopKo Stores, Inc.;

2. Based on my knowledge, this report does not contain any untrue statement of a
   material fact or omit to state a material fact necessary to make the
   statements made, in light of the circumstances under which such statements
   were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial
   information included in this report, fairly present in all material respects
   the financial condition, results of operations and cash flows of the
   registrant as of, and for, the periods presented in this report;

4. The registrant's other certifying officer(s) and I are responsible for
   establishing and maintaining disclosure controls and procedures (as defined
   in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over
   financial reporting (as defined in Exchange Act Rules 13a-15(f) and
   15d-15(f)) for the registrant and have:

   (a)  Designed such disclosure controls and procedures, or caused such
        disclosure controls and procedures to be designed under our supervision,
        to ensure that material information relating to the registrant,
        including its consolidated subsidiaries, is made known to us by others
        within those entities, particularly during the period in which this
        report is being prepared;

   (b)  Designed such internal control over financial reporting, or caused such
        internal control over financial reporting to be designed under our
        supervision, to provide reasonable assurance regarding the reliability
        of financial reporting and the preparation of financial statements for
        external purposes in accordance with generally accepted accounting
        principles;

   (c)  Evaluated the effectiveness of the registrant's disclosure controls and
        procedures and presented in this report our conclusions about the
        effectiveness of the disclosure controls and procedures, as of the end
        of the period covered by this report based on such evaluation; and

   (d)  Disclosed in this report any change in the registrant's internal control
        over financial reporting that occurred during the registrant's most
        recent fiscal quarter (the registrant's fourth fiscal quarter in the
        case of an annual report) that has materially affected, or is reasonably
        likely to materially affect, the registrant's internal control over
        financial reporting; and

5. The registrant's other certifying officer(s) and I have disclosed, based on
   our most recent evaluation of internal control over financial reporting, to
   the registrant's auditors and the audit committee of registrant's board of
   directors (or persons performing the equivalent functions):

   (a)  All significant deficiencies and material weaknesses in the design or
        operation of internal control over financial reporting which are
        reasonably likely to adversely affect the registrant's ability to
        record, process, summarize and report financial information; and

   (b)  Any fraud, whether or not material, that involves management or other
        employees who have a significant role in the registrant's internal
        control over financial reporting.

Date: June 3, 2005

                               /s/ Brian W. Bender
                               -------------------
                           By: Brian W. Bender
                           Title: Senior Vice President, Chief Financial Officer
                                  Co-Chief Executive Officer*

* The office of Chief Executive Officer is comprised of three executive
officers, each serving as Co-Chief Executive Officer.

                                       26