A large thrombus entrapped in an atrial septal defect is a rare condition that can lead to life-threatening systemic and pulmonary embolization. The use of thrombolysis may prove dangerous to the patient. Herein, we describe the emergency surgical management that contributed to a successful outcome in a 67-year-old man who was found to have a 23-cm-long thrombus across an atrial septal defect.