Aims To non-invasively assess intraventricular viscous energy loss (EL) and proportionality to kinetic energy (KE) in Fontan patients using 4D flow magnetic resonance imaging (MRI) and compare to healthy controls. Methods and results Thirty Fontan patients and 15 controls underwent 4D flow MRI. Ventricular EL was computed and normalized by end-diastolic volume (EDV). EL over the cardiac cycle (ELcycle) relative to the average kinetic energy (KEcycle) was quantified using a dimensionless index, ELindex (ELcycle/KEcycle). EL was significantly elevated in Fontan patients compared to controls (ELcycle/EDV: 3.7 vs. 2.6 J/m3, P = 0.001). Fontan patients with inflow of blood entering a ventricle, which leaves that ventricle through a ventricular septal defect to the aorta, defined as discordant inflow-to-outflow showed significantly higher EL compared to patients with inflow of blood into the same ventricle from which the blood is ejected into the aorta, defined as concordant inflow-to-outflow (ELcycle/EDV: 6.8 vs. 3.2 J/m3, P = 0.001). EL was not significantly different in Fontan patients with a systemic left vs. a systemic right ventricle (ELcycle/EDV: 3.5 vs. 3.6 J/m3, P = 0.91). ELindex was significantly elevated in Fontan patients compared to controls (ELindex: 0.4 vs. 0.2, P < 0.001). Highest ELindex was found in Fontan patients with discordant inflow-to-outflow compared to concordant inflow-to-outflow (0.5 vs. 0.3, P = 0.01). Conclusion Fontan patients show disproportionate intraventricular EL relative to KE. Intraventricular EL is elevated in these patients compared to healthy controls, and highest EL is found in patients with discordant inflow-to-outflow.