<PAGE>

                                                                   Exhibit 31.01

                    CERTIFICATION OF CHIEF EXECUTIVE OFFICER
                          UNDER RULE 13a-14(a) ADOPTED
                             PURSUANT TO SECTION 302
                        OF THE SARBANES-OXLEY ACT OF 2002

I, Michael A. Morache, President and Chief Executive Officer of PLATO Learning,
Inc., certify that:

1.    I have reviewed this Quarterly Report on Form 10-Q of PLATO Learning, 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 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)) for the registrant
      and we 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) 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 (c) disclosed in this report any change in the
      registrant's internal control over financial reporting (as defined in
      Exchange Act Rules 13a-15(f) and 15d-15(f)) 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.

5.    The registrant's other certifying officer 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 the registrant's
      board of directors: (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 9, 2005                         /s/ MICHAEL A. MORACHE
                                           -------------------------------------
                                           Michael A. Morache
                                           President and Chief Executive Officer