Fontan surgery and its modifications have improved survival in various forms of univentricular hearts. A regular atrial rhythm with atrioventricular synchrony is one of the most important prerequisite for the long-term effective functioning of this preload dependent circulation. A significant proportion of these survivors need various forms of pacing for bradyarrhythmias, often due to sinus nodal dysfunction and sometimes due to atrioventricular nodal block. The diversion of the venous flows away from the cardiac chambers following this surgery takes away the simpler endocardial pacing options through the superior vena cava. The added risks of thromboembolism associated with endocardial leads in systemic ventricles have made epicardial pacing as the procedure of choice. However challenges in epicardial pacing include surgical adhesions, increased pacing thresholds leading to early battery depletion and frequent lead fractures. When epicardial pacing fails, endocardial lead placement is equally challenging due to lack of access to the cardiac chambers in Fontan circulation. This review discusses the univentricular heart morphologies that may warrant pacing, issues about epicardial pacing, different techniques for endocardial pacing in patients with disconnected superior vena cava, pacing in different modifications of Fontan surgeries, issues of systemic thromboembolism with endocardial leads, atrioventricular valve regurgitation attributed to pacing leads and device infections. In a vast majority of patients following Glenn shunt and Senning surgery, an epicardial pacing and lead replacement is always feasible though technically very difficult. This article highlights the different options of transatrial and transventricular endocardial pacing.