Objective Patients with Fontan physiology may eventually require heart transplantation (HT). We determined the rates and outcomes of HT in a national, population-based multicentre study. Methods From 1990 to 2015, 1369 patients underwent the Fontan procedure as recorded in the Australia and New Zealand Fontan Registry. We identified those who underwent HT and analysed their outcomes. We compared rates of HT between two catchment areas. In area 1 (n=721), patients were referred to the national paediatric HT programme or its associated adult programme. In area 2 (n=648), patients were referred to the national paediatric HT programme or one of the other adult HT programmes. Results Mean follow-up time post-Fontan was 11±8 years. Freedom from Fontan failure was 74%±3.9% at 20 years. HT was performed in 34 patients. Patients living in area 1 were more likely to have HT (4.0%, 29/721 vs 0.8%, 5/648, p<0.001) with a cumulative proportion of 3.4% vs 0.7% at 10years and 6.8% vs 1.2% at 20years (p=0.002). Area 1 patients were more likely to undergo HT (hazard ratio 4.7, 95% CI 1.7 to 13.5, p=0.003) on multivariable regression. Post-HT survival at 1, 5 and 10years was 91%, 78% and 71%, respectively. Compared with other patients with congenital heart disease (n=87), Fontan patients had similar in-hospital outcomes and long-term survival. Conclusions Although HT after the Fontan procedure can be achieved with excellent outcomes, most patients with Fontan failure do not undergo HT. Significant regional differences in rates of HT in Fontan patients exist.