Abstract: More than thirty years after Congress passed the Religious Freedom Restoration Act, the extent of religious freedom enjoyed by military service members remains unsettled. Courts now largely agree that RFRA applies to the military. But scholars and judges disagree over the relationship between RFRA and the Commander-in-Chief power: Should courts follow RFRA’s text and impose strict scrutiny on the President’s decisions, or should they step aside in deference to executive control over the armed forces? This Article argues that history points the way to an answer—one that is, in other contexts, established and workable. Historically, Congress and the President handled religious accommodation internally—beginning with Congress’s creation of the chaplaincy and evolving through executive policies addressing particular religious needs. In repeated instances, Congress exercised its power to “make Rules” for the military by course-correcting the executive’s military religious freedom policies, and each time it did so, the executive acquiesced. Read against that historical pattern, the question of how to apply RFRA in the military is not the simple binary of executive versus judicial authority. It is instead a three-way separation-of-powers inquiry in which Congress has historically played the leading role. With this understanding, due deference to Congress means courts must scrutinize the military’s religious accommodation decisions under RFRA’s demanding test. Deciding such cases is still no easy task. Courts must determine what weight to give military professional judgment, balance government interests of the highest magnitude, and in some cases draw the line between RFRA’s protective sweep and the President’s prerogatives as Commander in Chief. But to answer those hard questions, courts should look to another area where they have traditionally deferred based on similar separation-of-powers concerns. As courts’ experience with prisoner cases shows, they already have a useful framework for applying RFRA in the military—one that respects both Congress’s intervention and the operational realities of military command.