Background We aimed to analyze mid-term outcomes of the fenestrated Fontan procedure, focusing on the fenestration size. Methods We retrospectively reviewed the outcomes of the fenestrated Fontan procedure. Among 165 patients who underwent the Fontan procedure from 2011 to 2021, fenestration was created in 27 patients with the highest risks, including those with hypoplastic left heart syndrome, hypoplastic pulmonary arteries, heterotaxy syndrome with high pulmonary vascular resistance, and pulmonary arterial pressure >15 mm Hg. The patients underwent the procedure at a median age of three years (body weight, 11.4 kg; body surface area, 0.54 m2). Fenestration sizes were 3.5 to 5 mm. Results Spontaneous fenestration closure occurred within one year postoperatively in nine patients. Among them, three experienced Fontan failure, necessitating refenestration. Although fenestration size did not differ, the size corrected by body surface area at the time of surgery was smaller in patients with fenestration closure (6.4 mm/m2 vs 8.3 mm/m2, P < .05). Patients with a fenestration <7 mm/m2 were more likely to have fenestration closure within one year postoperatively, and those with a fenestration >9 mm/m2 were more likely to have severe desaturation and require home oxygen therapy following discharge. Conclusions Spontaneous fenestration closure affected the frequency of Fontan complications. A very small fenestration size corrected by body surface area was a significant risk factor for spontaneous closure. Conversely, a very large fenestration size corrected by body surface area resulted in severe desaturation. The optimal fenestration size to prevent early spontaneous closure and severe desaturation is approximately 8 mm/m2.