Abstract Objectives Patients living with a Fontan circulation are prone to developing arrhythmia. However, their prognostic impact has been seldom studied. As such, we aimed to determine the incidence and predictors of arrhythmias after the Fontan procedure and the long-term outcomes of after first onset of arrhythmias. Methods Of the 1034 patients who have undergone a Fontan procedure as recorded in the Australian and New Zealand Fontan Registry, we identified those who developed either a tachyarrhythmia or bradyarrhythmia. We evaluated the incidence and predictors of developing arrhythmias and its prognostic impact on late outcomes. Results A total of 195 patients developed an arrhythmia. Tachyarrhythmia was present in 162, bradyarrhythmia in 74 while both forms were present in 41 patients. At 20 years, freedom from any arrhythmia, tachyarrhythmia and bradyarrhythmia was 68% (95% CI 59-72%), 69% (62-75%), and 85% (80-90%) respectively. On multivariable analyses, patients with an extra-cardiac Fontan (HR 0.23, 0.10-0.51, p<0.001) were less likely to develop an arrhythmia, while those with left atrial (HR 3.18, 1.45-6.95, p=0.004) and right atrial (HR 4.00, 2.41-6.61, p<0.001) isomerism were more likely to have an arrhythmia. After onset of any arrhythmia (tachy- or bradyarrhythmia), 10- and 15-year survival was 74% (65-83%) and 70% (60-80%) respectively and freedom from Fontan failure was 55% (44-64%) and 44% (32-56%). The development of any arrhythmia (HR 2.20, 1-44-3.34, p<0.001), tachyarrhythmia (2.56, 1.60-4.11, p<0.001) and bradyarrhythmia (1.85, 1.16-2.95, p=0.01) were all independent predictors of late Fontan failure on multivariable analyses. Conclusions The development of an arrhythmia is associated with a heightened risk of subsequent failure of the Fontan circulation.