A 19-year-old male with Fontan circulation developed protein-losing enteropathy associated with acute enteritis. Although his central venous pressure was in the normal range, subcutaneous high molecular heparin injection and oral predonisolone administration were not effective. We initiated intravenous high-dose methyl-predonisolone (15 mg/kg/day) for 3 days followed by oral predonisolone (0.5 mg/kg/day) for 4 days and repeated the course in 2 weeks. The serum protein and albumin increased to the normal level at 2 months after pulse therapy. The patient has not shown any recurrence of such protein-losing enteropathy for 2 years without any steroid agents.