<PAGE>

                                                                    EXHIBIT 31.1
                            SECTION 302 CERTIFICATION

I, Janice P. Anderson, certify that:

1.    I have reviewed this quarterly report on Form 10-Q of Onyx Software
      Corporation;

2.    Based on my knowledge, this quarterly 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 quarterly report;

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

4.    Onyx'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)) and internal controls over financial
      reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for
      Onyx 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 Onyx,
            including its consolidated subsidiaries, is made known to us by
            others within those entities, particularly during the period in
            which this quarterly 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 Onyx's disclosure controls and
            procedures and presented in this quarterly report our conclusions
            about the effectiveness of the disclosure controls and procedures,
            as of the end of the period covered by this quarterly report based
            on such evaluation; and

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

5.    Onyx's other certifying officer and I have disclosed, based on our most
      recent evaluation of internal controls over financial reporting, to Onyx's
      auditors and the audit committee of Onyx'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 Onyx'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 Onyx's internal
            control over financial reporting.

Date: May 10, 2006

                                        By:     /s/  JANICE P. ANDERSON
                                             -----------------------------------
                                                      JANICE P. ANDERSON
                                                 CHIEF EXECUTIVE OFFICER AND
                                                    CHAIRMAN OF THE BOARD