The primary objective of this study was to ascertain the long-term health-related quality of life (HRQOL) of adult patients who underwent a childhood Fontan operation for palliation of univentricular cardiac anomalies. The secondary objective was to compare the long-term HRQOL of Fontan survivors to that of pediatric heart transplant recipients. This cross-sectional study examined adult survivors (>19 years) who underwent a Fontan operation during childhood (Fontan group) or a pediatric heart transplant (HT group) between 1988 and 2011 (23-year span). HRQOL was assessed using the short form 36 survey. The study group consisted of 49 Fontan group patients and 13 HT group patients who responded to the survey. HRQOL scores of the Fontan group were similar to those of an age-controlled healthy US population in social and mental functioning, energy or vitality, and overall mental component score (P ≥ 0.2). However, Fontan scores in physical functioning, bodily pain, general health, and overall by physical component were significantly lower than those of the age-controlled US population (P < 0.05). No differences were identified between Fontan and HT patients. This favorable life-satisfaction period (average 18 years) should be considered when informing patients and families of expectations with the Fontan pathway vs certain higher-risk procedures.