A 9.5-year-old girl after Fontan procedure for hypoplastic left heart syndrome had recurrent protein-losing enteropathy (PLE) develop 2 months after partial catheter closure of the Fontan fenestration. Despite satisfactory hemodynamic measurements under general anesthesia, we postulated that she suffered from increased pulmonary vascular reactivity and commenced her on Sildenafil treatment. After 6 weeks of oral Sildenafil treatment, her serum albumin and the fecal alpha-1-antitrypsin levels normalized, and her exercise tolerance had increased. There was also an improvement of the mesenteric arterial flow patterns on Doppler studies. Sildenafil should be considered in the treatment of PLE after the Fontan procedure.