Four-dimensional flow magnetic resonance imaging (4D flow MRI) visualizes three-dimensional pulsatile blood flow and allows quantification of the mechanical stress to the cardiovascular system. We report a case of total cavopulmonary connection (TCPC) with a kinked extracardiac conduit in a 14-year-old boy with protein-losing enteropathy (PLE), for which a 4D flow MRI assessment of hemodynamics proved useful. Aged 2 years, the patient underwent extracardiac TCPC with an 18-mm expanded polytetrafluoroethylene conduit for a single right ventricle and pulmonary atresia. He developed PLE 3 years later, which was controlled with steroids. Aged 14 years, computed tomography revealed a kinked conduit with calcification. Cardiac catheterization showed no drop in pressure in the kinked portion, but the mean pulmonary arterial and right ventricular end-diastolic pressures were elevated. A systemic right ventricular pressure curve demonstrated a slow pressure decrease in the isovolumic relaxation phase, with a prolonged time constant, and 4D flow MRI demonstrated no flow acceleration through the kinked portion or in the systemic ventricle, with sufficient low-flow energy loss. We decided initially to optimize the patient’s medication to improve diastolic dysfunction, and then to perform a conduit exchange in the future once the steroid dose was reduced.