Protein-losing enteropathy (PLE) is a life-threatening complication in patients following the Fontan operation. However, PLE also develops in some patients with congenital heart disease (CHD) after biventricular repair (BVR). This study compared clinical profiles of PLE patients following the Fontan operation with those after BVR. We retrospectively reviewed clinical charts of postoperative CHD patients with PLE. The study population comprised 42 PLE patients (14BVR, 28Fontan). Postoperative follow-up period until onset was significantly shorter in the Fontan group than in the BVR group (14 ± 2 vs. 8 ± 1 years, p = 0.02), while there was no difference in PLE onset age between groups. Furthermore, there were no differences in prevalence of clinically relevant arrhythmias, cardiac output, or central venous pressure between the two groups at PLE onset. Percentage of structural lesions (valve regurgitation and/or stenotic lesions) responsible for development of PLE and ventricular end-diastolic pressure were higher in the BVR group than in the Fontan group (93 vs. 50%, p < 0.01), (13.4 ± 6.3 vs. 7.5 ± 4.1, p < 0.0001). Catheter intervention was applied in 2Fontan and 6BVR patients, while surgical intervention was required in 8BVR and 7Fontan patients. Of these, catheter intervention was effective in 2 (25%, 1Fontan, 1BVR) and surgical intervention was effective in 4 (26.7%, 1Fontan, 3BVR). Only one patient (5.3%) improved without intervention. Complete PLE remission rate was higher in the BVR group than in the Fontan group (38 vs. 7%, p = 0.02). During follow-up, death of 2 BVR and 8 Fontan patients occurred. There were no group differences in 5- to 10-year survival rates after PLE onset (81 vs. 81%, BVR, 81 vs. 66%, Fontan). Although BVR patients may have greater chance of PLE remission when compared with those exhibiting Fontan pathophysiology, mortality in PLE-CHD patients was significantly high regardless of postoperative hemodynamics.