Since Huntington’s seminal work The Soldier and the State, the scholarship on civil–military relations in the American context has often emphasized the need for a professional military to maintain an apolitical stance and let the civilian principals lead. In this article, we ask, what can we learn about civil-military relations by seeking to better understand the relationship between political institutions and the politicization of the military? We argue that this literature insufficiently accounts for the perils that exist within separation of powers (i.e., presidential) systems. Consequently, the existing scholarship cannot distinguish when politicization happens because of or despite civilian principals. We use long-standing arguments from Comparative Politics to explain why problems of separation of powers systems are endemic to these institutions. We then present five questions and two examples to facilitate a theoretical reframing of the subject. Our argument suggests more work is needed to understand how American political institutions shape civil–military relations.