Post-myocardial infarction ventricular septal perforation (VSP) is one of the lethal complications of transmural myocardial infarction. Although the treatment of VSP mostly requires surgical procedures using heterologous pericardium, thromboembolism rarely occurs in patients who undergo VSP repair. Herein we report the case of a patient who died of sudden massive cerebral infarction two weeks after the surgery. The autopsy findings revealed concaved mural LV thrombus in the dissected heart. It is suspected that the patient died of extensive cerebral infarction due to thromboembolic occlusion of the carotid or central cerebral artery. In the postoperative period after VSP repair, several risk factors for thrombus formation may occur, such as postoperative hypercoagulability due to systemic inflammation by the high operative invasiveness, the presence of foreign material in the impaired left ventricle, or pericardial patch suturing methods. Our clinical experience indicates that meticulous postoperative management may be needed, keeping LV thrombus formation in mind after VSP repair.