A 23-year-old woman with mitral valve infective endocarditis complicated by embolism of the right common iliac artery underwent transfemoral embolectomy by a Fogarty catheter and mitral valve replacement. She developed occlusion of the right internal iliac artery, that was revealed by computed tomography on the 9th postoperative day. The occlusion was considered to result from migration of a part of the emboli from the right common iliac artery into the right internal iliac artery during the procedure of embolectomy. On the 16th postoperative day, she underwent repeat mitral valve replacement because of perivalvular leakage. Furthermore, after 2 weeks from the diagnosis of embolism of the right internal iliac artery, the embolic site showed aneurysmal formation finally requiring aneurysmectomy. Her recovery was uneventful. Our case is considered to be rare in that serial observations on computed tomography indicated the development of mycotic aneurysm at the site of septic embolism. In addition, care must be taken to prevent migration of emboli into branched arteries during the procedure of embolectomy for peripheral arterial septic embolism caused by infective endocarditis.