Up to 10% of Fontan patients require pacemakers; an epicardial approach has historically been used. A transvenous approach can be used but carries risk of Fontan obstruction, thromboembolism, and can be technically challenging. The safety and efficacy of these approaches is not well described. The aim of this study was to compare epicardial and transvenous pacemaker outcomes in Fontan patients, specifically, device performance and adverse event rate. A retrospective review was performed on Fontan pacemaker patients followed at a single institution. Thirty-one Fontan pacemaker patients were identified between 1985 and 2017. Twenty-six had an epicardial system, five transvenous, and three converted from epicardial to transvenous. Average atrial lead sensing at placement was 3.23 versus 2.35 mV (p = 0.52) for epicardial and transvenous leads, respectively. Median atrial and ventricular lead longevity was 86.4 versus 98.8 months (p = 0.56) and 73.2 versus 140 months (p = 0.3) with generator longevity of 65.5 versus 73.9 (p = 0.16) months for epicardial versus transvenous systems, respectively. One major complication occurred in a transvenous patient, and two minor complications occurred in epicardial patients. All transvenous patients received warfarin except one, who converted to dabigatran. Epicardial patients received aspirin (n = 20), warfarin (n = 3) or a warfarin/aspirin combination (n = 3). No thromboembolic events occurred. System revision was required in 13 epicardial and 5 transvenous patients. There were two deaths, none related to the pacemaker system. Transvenous pacemakers can be utilized with equal efficacy compared to epicardial pacemakers with trends toward longer lead longevity in transvenous pacemaker systems.