Left ventricle to right atrial communication is a rare cardiac pathology, and it is either congenital or acquired. Recently, case reports of acquired left ventricle to right atrial communication have been increasing because of the increased numbers of cardiovascular procedures and improved cardiac diagnostic techniques. We report a case of acquired left ventricle to right atrial communication in a patient with native aortic valve infective endocarditis. A 52-year-old man with worsening dyspnea on exertion and lower leg edema was admitted to a hospital. Blood examination revealed elevated inflammatory marker levels, and transthoracic echocardiography (TTE) showed an aortic valve vegetation. The patient was subsequently transferred to our hospital for infective endocarditis with congestive heart failure. Medical treatment with antibiotics and diuretics was initiated. Cardiac computed tomography (CT) demonstrated left ventricle to right atrial communication. An urgent operation was performed wherein the defect was closed with autologous pericardial patches from both the right atrium and left ventricle. Aortic valve replacement was performed with a mechanical valve. The postoperative course was uneventful, and TTE showed no residual shunt. In our case, cardiac CT was useful for accurately diagnosing left ventricle to right atrial communication.