A 63-year-old woman presented with chest discomfort. Coronary angiography revealed vasospastic angina. Cardiac multi detector computed tomography and cardiac magnetic resonance imaging showed a 30 × 30-mm atrial septal aneurysm (ASA) protruding into the right atrium and thrombus attached to the left side of the ASA pouch. We surgically resected the ASA because the patient was at risk for systemic thrombosis. The resection site was closed with pericardial patch through a median sternotomy under a cardiopulmonary bypass. The postoperative course was uneventful, and the patient was discharged on postoperative day 26.