As a combat support agency within the Department of Defense, DTRA reports to the ​​​Under Secretary of Defense for Acquisition and Sustainment, formerly USD (AT&L). This reorganization occurred in August of 2017 and is currently under implementation during Fiscal Year 2019..

DTRA is led by a senior civil servant, a member of the Senior Executive Service (SES). DTRA also has a Deputy Director for Combat Support, a Vice Director for Mission Integration, a Vice Director for Plans & Programs, and a Command Senior Enlisted Leader, responsible for offering an enlisted perspective on operational issues and missions.