We estimated the inpatient resource use for a Fontan patient from birth to adulthood and explored factors that might induce cost differences (2014 US dollar). Inpatient costing records from 4 hospitals with greatest numbers of Fontan patients in Australia and New Zealand were linked with the Fontan registry database. Inpatient records between July 1995 and September 2014 for 420 Fontan patients were linked, and the most frequent primary diagnoses were hypoplastic left heart syndrome (20.7%), tricuspid atresia (19.7%), and double inlet left ventricle (17.1%). The mean hospital cost for a Fontan patient from birth to 18 years of age was estimated to be $390,601 (95% confidence interval [CI] $264,703 to $516,499), corresponding to 164 (95% CI 98 to 231) inpatient days. The cost incurred from birth through to Fontan completion (the staged procedures period) was $219,482 (95% CI $202,410 to $236,553) and the cost thereafter over 15 years was $146,820 (95% CI $44,409 to $249,231), corresponding to 82 (95% CI 72 to 92) and 65 (95% CI 18 to 112) inpatient days, respectively. Costs were higher in male and hypoplastic left heart syndrome patients in the staged procedures period (p <0.001). Having fenestration was associated with higher costs in the staged procedures period (p <0.001) and lower cost after Fontan over 15 years (p = 0.66). In conclusion, patients with single ventricle congenital heart disease continue to demand considerable inpatient resources after the staged procedures period. Over 40% of the pediatric hospital costs for Fontan patients were estimated to occur after the last planned surgery.