EXHIBIT 31.2

SECTION 302 CERTIFICATION

I, Paul D. Borja, certify that:

1) I have reviewed Amendment No. 1 to Annual Report on Form 10-K of Flagstar Bancorp, Inc. (the registrant);

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) [omitted];

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 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 the 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 registrants internal control over financial reporting that
occurred during the registrants most recent fiscal quarter (the registrants 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 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 function):

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 30, 2013 |  |  |  | /s/ Paul D. Borja                                   
|                     |  |  |  | Paul D. Borja                                       
|                     |  |  |  | Executive Vice-President and Chief Financial Officer