An 81-year-old woman with arrhythmogenic right ventricular cardiomyopathy underwent catheter ablation for atrial fibrillation and atrial flutter. Hypoxemia refractory to the administration of oxygen was seen after transseptal puncture. Transthoracic echocardiography revealed right to left shunt via an iatrogenic atrial septal defect (IASD) that was increased by tricuspid regurgitation flow. Her hypoxemia improved after IASD occlusion with the inflation of a venogram balloon catheter. Emergent surgical IASD closure was successfully performed. IASD after transseptal puncture for atrial fibrillation ablation infrequently causes severe complications that require emergent repair.