The optimal management strategy for atrial tachyarrhythmia in the Fontan population is unknown. Methods Retrospective review of 264 adult Fontan patients with atrial tachyarrhythmia evaluating 3 clinically adopted scenarios: antiarrhythmic drug (AAD) therapy, catheter ablation (CA), and Fontan conversion (FC). These patients were followed up at Mayo Clinic from 1994 to 2014. The study objective was to compare freedom from atrial tachyarrhythmia recurrence (AR) and occurrence of composite adverse events (stroke, heart failure hospitalization, death, or heart transplant) between treatment groups. Results The age of atrial tachyarrhythmia onset was 25 ± 4 years, time from Fontan operation was 13 ± 6 years, follow-up was 74 ± 18 months, atriopulmonary Fontan was 215 (81%), and atrial flutter/intra-atrial reentry tachycardia was 173 (65%). In those managed with AAD (n = 110), freedom from AR was 7% at 60 months. Catheter ablation (n = 31) was associated with an acute procedural success of 94%, and freedom from AR was 41% at 60 months. Fontan conversion (n = 33) resulted in a perioperative mortality of 3%, and freedom from AR was 51% at 60 months. Fontan conversion and CA were similar with regard to AR (P = .14) and significantly better compared with AAD (P < .0001). Adverse events were found to occur more frequently in the patients with AR (P < .0001) and the patients treated with AAD only (P < .0001). Conclusions Catheter ablation and FC operations are associated with less recurrence of atrial tachyarrhythmia compared with AAD. Atrial tachyarrhythmias are more likely to recur in patients with a longer history of the arrhythmia and are associated with more adverse events. Early referral to a specialty center for these interventions should be considered.