Placement of an epicardial pacemaker system is often preferred over an endocardial system in patients who have undergone a Fontan operation, but data are limited on how these two systems perform over time in patients with Fontan palliation. We performed a retrospective review of adults with Fontan palliation who had pacemaker implantation and interrogation data at Mayo Clinic from 1994 to 2014. Lead parameters, pacing mode, and polarity were collected at the earliest device interrogation report. Clinic notes and device interrogation reports were reviewed at implantation, 6 months, and yearly after implantation to determine impedance, capture threshold (CT), and energy threshold (ET). There were 87 patients with 168 leads in the study cohort. The mean follow-up time was 7.7 years (6 months–19 years). There were 143 epicardial leads (57 atrial and 86 ventricular) and 25 endocardial leads (20 atrial and 5 ventricular). There was no difference in the baseline lead parameters between epicardial and endocardial leads for impedance (610 ± 259 versus 583 ± 156 Ω, p = 0.93), CT (2.0 ± 1.3 versus 1.8 ± 1.3 V, p = 0.28), or ET (7.1 ± 12.5 versus 6.8 ± 18.1 µJ, p = 0.29). Compared to endocardial leads, ventricular epicardial leads were associated with temporal decrease in impedance and increase in ET. Regarding clinical outcomes, epicardial leads had higher rates of failure but similar generator longevity in comparison to endocardial leads. Ventricular epicardial leads were associated with temporal decrease in impedance and increase in ET. Epicardial leads had a higher rate of failure but similar generator longevity compared to endocardial leads.