Nationwide registry data of patients with single-ventricle physiology have been rarely reported. The Medical Aid Program for Chronic Pediatric Diseases of Specified Categories (Japan) has contributed to the financial support of medical expense for patients younger than 20 years with chronic paediatric disease, and almost all children in Japan who require disease-specific treatment voluntarily apply to this programme. The epidemiology and medium- to long-term outcome of patients following a Fontan procedure were investigated using the database. The usefulness of this epidemiologic investigation in identifying real-world objectives and clinical applications was also examined. A total of 2862 patients who underwent a Fontan operation were identified from 18,589 patients with chronic heart disease registered to the medical aid programme. The details of symptoms, treatment, and somatic growth were evaluated, from which we were able to clarify the nationwide data regarding the current status of post-Fontan patients younger than 20 years. This study elucidated the current status of post-Fontan patients under 20 years of age in Japan. Data analysis of the Medical Aid Program for Chronic Pediatric Diseases of Specified Categories cohort provided useful information towards understanding the comprehensive status of patients with chronic heart disease and contributed to improved disease management.