Background: Although the Fontan procedure is associated with a variety of long-term complications, it is the mainstay treatment for congenital heart disease with a functioning single ventricle. Data concerning the epidemiological profile are scarce. Methods: We investigated the current epidemiological profile using a 2000-2008 nationwide birth cohort from a 2000-2014 database (1,967,991 live births), with complete postnatal data for at least 6 years. We identified 363 patients (2792 patient-years of follow-up) who had received the Fontan procedure, giving an incidence of 0.184/ 1000 live births. Results: The overall Fontan surgical survival rate was 81.8%. In post-Fontan patients, the 10-year survival was 0.822 (0.026). Causes of death included cardiac (43.8%), infection (20.8%), out-of-hospital death (16.7%), sudden death (8.3%), cerebral vascular accident (8.3%) and malignancy (2.1%). The risk of unexpected death (sudden death and out-of-hospital death) was 4.0%, or 0.55% per post-Fontan patient-year. Arrhythmias were common (12.1%). Supraventricular tachycardia was the most common type of arrhythmia, and occurred prior to the Fontan procedure in 22 patients, with a cumulative risk of 2.2%, 6.3%, and 11.6% by the age of 1, 5 and 10 years, respectively. Arrhythmia intervention was performed in 40.9% of those with arrhythmia, including electrophysiological studies/ ablation in 12 and device therapy in 6 patients. Conclusions: In conclusion, the incidence of Fontan patients was 0.184/1000 live births. Their medical complexity included a high risk of supraventricular tachycardia and unexpected death by adolescence.