Background Patients with functional single ventricle (SV) are at risk for adverse outcomes after staged palliation from the superior cavopulmonary connection (SCPC) to the Fontan. Current pre‐Fontan assessment by cardiac magnetic resonance and cardiac catheterization includes measuring atrioventricular valve regurgitation, aortopulmonary collateral burden, and pressures. Four‐dimensional flow can quantify complex flows representing hemodynamic inefficiency. This study determined the clinical significance of kinetic energy (KE) and viscous energy loss in patients before the Fontan procedure using 4‐dimensional flow. Methods and Results This was a retrospective analysis of patients before the Fontan procedure who underwent ferumoxytol‐enhanced cardiac magnetic resonance and same‐day catheterization. Four‐dimensional flow data sets were analyzed using ITFlow (CardioFlowDesign) to measure KE/viscous energy loss in the atrium, SV, and SCPC. A composite outcome was defined by rejected Fontan candidacy, prolonged hospitalization, lymphatic dysfunction, or heart failure. The relationship between these outcomes and KE/viscous energy loss was assessed by bivariable and multivariable logistic regression analyses as appropriate. Sixty‐five patients (3.9±1.5 years, 0.64±0.1 m 2 ) were included. Fifty (77%) proceeded to Fontan operation with median hospitalization time of 8.5 (interquartile range, 7–12.7) days. Twenty‐six (40%) experienced a composite outcome, including 9 with rejected candidacy. Lower SCPC flow was associated with an outcome ( P =0.042). Meanwhile, higher SV KE and lower SCPC KE were independently associated with composite outcome (odds ratio, 3.63 [95% CI, 1.32–13.2]; P =0.0263; odds ratio, 0.906 [95% CI, 0.814–0.980]; P =0.0377). Higher SV KE and lower SCPC KE corresponded to significant atrioventricular valve regurgitation, higher aortopulmonary collateral burden, and higher cathetherization pressures. Conclusions Four‐dimensional flow analysis provides insight into SV hemodynamics and is associated with short‐term outcomes. Future work will analyze the longitudinal implications for patients undergoing the Fontan procedure.