Flow energy loss (EL) at the Fontan anastomosis has been thought to reflect flow efficiencies and to influence on hemodynamics in the Fontan circulation and has been often discussed in numerical studies. However, in vivo EL measurements have to date not been reported. We directly measured EL in the Fontan circulation and examined the relationship between the structural configuration and EL, as well as the influence of EL, on the hemodynamics in the Fontan circulation. We performed a catheterization study measuring simultaneous pressure and flow velocity to calculate EL in nine patients (mean age 2.3 ± 0.3 years) 1 year after the Fontan procedure. The measured EL was 9.66 ± 8.50 mW. One patient with left pulmonary artery stenosis recorded the highest EL (17.78 mW), and one patient with bilateral superior vena cava and left phrenic nerve palsy recorded the second highest EL (14.62 mW). EL significantly correlated with time constant tau and weakly with max-dp/dt during the isovolumic diastolic phase (r = 0.795 and -0.574, respectively). EL also correlated with max-dp/dt during the isovolumic systolic phase (r = 0.842) but not with ejection fraction or systemic blood flow (r = 0.384 and -0.034, respectively). In conclusion, inefficient structural configuration and phrenic nerve palsy seem to be related with increased in EL at the Fontan anastomosis. Although these preliminary findings also suggest that EL is associated with an impaired relaxation of the ventricle, a long-term study with a large population is warranted to reach such a definitive conclusion.