<PAGE>
                                                                    Exhibit 31.2

    Certification of Chief Financial Officer Pursuant to Rule 13a-14(a) of the
    Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the
    Sarbanes-Oxley Act of 2002

I, Brian C. Henry, certify that:

    1. I have reviewed this annual report on Form 10-K of Cray 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)) and internal control over financial
reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) 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) 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 the 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 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 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 (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: April 20, 2006

                                      /s/  BRIAN C. HENRY
                                      --------------------------------
                                           Brian C. Henry
                                           Chief Financial Officer