Protect Troops at War Act of 2013 - Amends the Balanced Budget and Emergency Deficit Control Act of 1985 to eliminate for FY2013-FY2014 the reductions to discretionary appropriations or direct spending for the defense function of the Department of Defense (DOD). Requires the reductions that would otherwise have occurred to be added to and distributed equally among the sequestration for such function for FY2015-FY2021.

Authorizes the Secretary of Defense to transfer amounts appropriated for DOD by the Continuing Appropriations Resolution among DOD accounts. Requires account amounts, after such transfer, to be consistent with amounts appropriated or authorized for such accounts under a DOD appropriations or authorization Act for FY2013. Requires 15 days' advance notice of such transfers to the congressional defense and appropriations committees.