Many argue that during conflict, executive power expands at the expense of the judiciary and civil liberties. Although this is a common conjecture, no systematic study of conflict and judicial independence exists. We argue that conflict, rather than strictly inhibiting independence, is instead a critical juncture that increases the possibility of institutional change, either positive or negative. We assess this claim in three ways: cross-national analyses of (1) de facto and (2) de jure judicial independence after the onset of conflict, and (3) a case study of statutory and jurisdictional changes to the federal judiciary after the outbreak of the U.S. Civil War. Each illustrates that conflict onset is associated with a higher likelihood of changing levels—both decreases and increases—rather than unidirectional decreases in judicial independence. We then present preliminary hypotheses and analyses for three factors that, given conflict onset, should be associated with either improved or worsened conditions for the judiciary. This study has implications for research on conflict, courts, and the rule of law in both political science and legal studies.