Iatrogenic atrial septal defect is an issue after percutaneous interventions for structural heart disease. A 63-year-old man, who had previously received 5 catheter ablations for paroxysmal atrial fibrillation, was found to have an iatrogenic atrial septal defect that persisted after the fourth intervention. Approximately 4 years later, he suffered exertional dyspnea. Pulmonary hypertension was caused by a left-to-right shunt via a large iatrogenic atrial septal defect. We performed surgical closure and the symptom improved. The timing of treatment for persistent iatrogenic atrial septal defect is difficult to determine, but preferable before the appearance of right ventricular dysfunction or embolism.