Considering the increasing dependence of EU politics from the domestic context of member-states, this theoretical essay suggests that we need to rethink EU referenda’s legitimacy both at national and supranational levels, and according to the type of the referendum. Unlike research on EU referenda that is mostly informed by direct democracy, the paper employs the agonistic democracy approach due to the latter’s normative imperative for citizens to have an effective say in their governance. Discussion proceeds as follows. The first section critically comments on seminal readings of EU legitimacy. The section that follows presents the basic features of agonistic democracy, and its value-added for assessing EU referenda’s legitimacy. The third section comparatively explores the recent Greek and British EU referenda to demonstrate ensuing legitimacy problems at national and supranational levels. The concluding remarks capitalize on the present analysis to raise broader reflections on legitimacy issues in the EU.