The few studies evaluating data on resource utilisation following the Fontan operation specifically are outdated. We sought to evaluate resource utilisation and factors associated with increased resource use after the Fontan operation in a contemporary, large, multi-institutional cohort. This retrospective cohort study of children who had the Fontan between January, 2004 and June, 2013 used the Pediatric Health Information Systems Database. Generalised linear regression analyses evaluated factors associated with resource use. Of 2187 Fontan patients included in the study, 62% were males. The median age at Fontan was 3.2 years (inter-quartile range (IQR): 2.6–3.8). The median length of stay following the Fontan was 9 days (IQR: 7–14). The median costs and charges in 2012 dollars for the Fontan operation were $93,900 (IQR: $67,800–$136,100) and $156,000 (IQR: $112,080–$225,607), respectively. Postoperative Fontan mortality (30 days) was 1% (n=21). Factors associated with increased resource utilisation included baseline and demographic factors such as region, race, and renal anomaly, factors at the bidirectional Glenn such as seizures, valvuloplasty, and surgical volume, number of admissions between the bidirectional Glenn and the Fontan, and factors at the Fontan such as surgical volume and age at Fontan. The most strongly associated factors for both increased Fontan length of stay and increased Fontan charges were number of bidirectional Glenn to Fontan admissions (p<0.001) and Fontan surgical volume per year (p<0.001). As patient characteristics and healthcare-related delivery variables accounted for most of the factors predicting increased resource utilisation, changes should target healthcare delivery factors to reduce costs in this resource-intensive population.