Audit the Pentagon Act of 2013

Audit the Pentagon Act of 2013 - Provides that Department of Defense (DOD) financial statements shall cease to be covered by specified DOD financial reporting requirements upon the issuance of an unqualified audit opinion (UAO) on such statements.

Provides that if DOD obtains a UAO on its statement of budgetary resources for any fiscal year after FY2014, the limitation on the total amount of authorizations that the Secretary of Defense may transfer pursuant to general transfer authority in the national interest in the succeeding fiscal year shall be $8 billion. Sets forth thresholds for the reprogramming of funds that shall apply to increases or decreases to the program base amount for a procurement or research program or an operation and maintenance or military personnel budget activity for a military department, defense agency, or defense field activity that obtains a UAO on its statement of budgetary resources.

Requires additional qualifications and responsibilities of the Under Secretary of Defense (Comptroller) and certain other DOD financial management officials if DOD fails to obtain a UAO on its general fund statement of budgetary resources for FY2015 by December 31, 2015.

Provides that if DOD fails to obtain a UAO on its general fund statement of budgetary resources for FY2018 by December 31, 2018, the reprogramming authority provided above will cease to apply. Requires, effective as of April 1, 2019, the reorganization of the position of DOD Chief Management Officer, with added qualifications and responsibilities.

Transfers jurisdiction of the Defense Finance and Accounting Service from DOD to the Department of the Treasury and requires the Secretary of the Treasury to administer such Service.

Provides that if a military department fails to obtain a UAO on its financial statements: (1) for FY2018 by December 31, 2018, the reprogramming authority provided above will cease to apply; and (2) for any fiscal year after 2017, amounts available to that department may not be obligated for a weapon or weapon system or platform being acquired under a major defense acquisition program for any activity beyond Milestone B approval not already obtained.

Directs the Secretary of Defense to amend the acquisition guidance of DOD to place specific limits on the procurement of any enterprise resource planning business system, including a three-year limit on its total procurement time from initial obligation of funds to full deployment and sustainment.