The extracardiac conduit (ECC) modification of the Fontan procedure has been theorized to reduce the risk of sinus node dysfunction and atrial arrhythmia compared with the intraatrial lateral tunnel (ILT) Fontan. This study aimed to compare the prevalence of early and late arrhythmias in patients who underwent ECC and ILT Fontan from a similar era with long-term follow-up at a single institution. A retrospective cohort study was conducted of all patients who underwent ECC or ILT Fontan from 1995 to 2005 at The Children's Hospital of Philadelphia. Bradyarrhythmias (including sinus node dysfunction), tachyarrhythmias, and pacemaker burden prevalence was determined throughout early (<30 days) and late (>30 days) postoperative periods. Of 434 patients undergoing the Fontan procedure during the study period, a total of 87 and 106 patients who underwent ECC and ILT Fontan, respectively, met the inclusion criteria. There were no significant differences in risk of sinus node dysfunction or tachyarrhythmia in both early and late postoperative periods. Although the overall risk of late postoperative pacemaker therapy was lower for the ECC cohort (4.9% vs 15.7%, p = 0.03), when adjusting for follow-up time, no significant difference was observed (odds ratio 3.1, 95% confidence interval 0.6 to 15.2, p = 0.16). In conclusion, the overall prevalence of late postoperative arrhythmias observed after contemporary Fontan modifications is low. Intra-atrial reentrant tachycardia, a potentially fatal complication of the atriopulmonary Fontan operation was infrequently encountered in both ECC and ILT Fontan cohorts. Pacemaker use was higher in the ILT group, although this difference may be explained by differences in follow-up time. Despite the low prevalence of arrhythmias after contemporary Fontan modifications, ongoing surveillance is warranted as the onset of arrhythmias may emerge after longer follow-up time.