A 50-year-old man was transferred to our hospital for investigation of cerebellar infarction, thought to have been caused by cardiac thromboembolism. We assumed that the cardiac thromboembolism had occurred as a late complication of a percutaneous transvenous mitral commissurotomy (PTMC) performed 7 years earlier. An echocardiogram and thoracic computed tomography revealed a protruding thrombus in the left atrium and an emergency operation was performed. The protruding thrombus was found to originate from the scar that penetrated into the intra-atrial muscular septum caused by the PTMC. After removing the thrombus, the scar was covered with normal endothelium and the mitral valve was replaced with a 27-mm St. Jude Medical prosthetic valve. We think that the thromboembolism was caused by mitral valve restenosis, atrial fibrillation, and endothelial injury in the interatrial septum during PTMC. Therefore, long-term follow-up and appropriate medication is recommended after PTMC, since restenosis and thrombosis are likely to occur.