Although bronchogenic cysts are the most common primary mediastinal cysts, intracardiac bronchogenic cysts are extremely rare. We report a case of a bronchogenic cyst of the interatrial septum in a 42-year-old woman who presented with recent onset of dyspnea on exertion. Cardiac investigations including transthoracic echocardiography and computed tomography revealed a cystic homogeneous mass in the interatrial septum. The patient underwent surgical resection, and the resultant atrial septal defect was repaired using an autologous pericardial patch. Histopathological examination of the resected specimen revealed findings consistent with a benign bronchogenic cyst. Although bronchogenic cysts are extremely rare, they should be considered in the differential diagnoses of intracardiac tumors. Complete resection of bronchogenic cysts is recommended primarily for diagnostic and potentially therapeutic purposes.