Protein-losing enteropathy occurs in up to 10% of patients following the modified Fontan procedure. Treatment is still controversial. We describe a female adolescent who developed protein-losing enteropathy 4 years after a modified Fontan procedure. Treatment with oral prednisone attenuated the protein loss with subsequent normalization of her serum total protein and albumin levels. Discontinuation of prednisone therapy was associated with relapse, which was again treated successfully with low-dose oral prednisone. Small bowel biopsy-proved diagnosis with improvement, relapse, and improvement again are documented, as are other useful laboratory findings.