The study aimed to assess the long-term outcomes after fenestration closure in patients at risk for Fontan failure. Of 119 patients who underwent Fontan operation between 1995 and 2004, fenestration was not created in 89 patients (NF group) and created in 30 patients with hypoplastic left heart syndrome, heterotaxy syndrome, high pulmonary arterial pressure, high systemic ventricular end-diastolic pressure, low ventricular ejection fraction, or atrioventricular valve regurgitation. All fenestrations were closed spontaneously or by catheter/surgical interventions, excepting two patients, and therefore, they were excluded. In fenestration group, patients with pre-Fontan mean pulmonary arterial pressure ≥ 15 mmHg or systemic atrioventricular valve regurgitation ≥ moderate were classified as high-risk Fontan candidates (F-HR group, n = 16), and the remaining patients were as standard-risk (F-SR group, n = 12). Protein-losing enteropathy-free survival rates did not differ among the three groups (p = 0.72). Serial follow-up catheter examinations after Fontan operation were completed in 69 patients in NF group and 11 patients in both F-SR and F-HR groups. Cardiac index and pulmonary vascular resistance significantly and similarly decreased over time in all groups, though the F-HR group showed lowest arterial oxygen saturation, lowest cardiac index, and highest pulmonary vascular resistance. The F-HR group also showed much veno-venous collaterals (p = 0.049), low peak oxygen consumption (p = 0.019), and low anaerobic threshold (p = 0.023) as compared to those in the F-SR group. In F-HR group, cyanosis remained after fenestration closure due to transformation from fenestration to veno-venous collaterals, which resulted in elevation of pulmonary vascular resistance, low cardiac index, and deterioration of exercise tolerance.