A 50-year-old man presented with shortness of breath. The patient underwent ventricular septation for a single ventricle with L-malposition of the great arteries at 6 years of age. Examinations revealed that the calcified patch for septation was torn and perforated, resulting in a left-to-right shunt. We report a rare case of a single ventricle who survived after septation 40 years ago and underwent the reoperation due to a torn calcified patch.