A 24-year-old man was admitted due to fever for two days. He had undergone modified Bentall operation at the age of 18. Transthoracic echocardiography (TTE) showed no findings of infective endocarditis (IE), and he was treated with a course of antibiotics. On the next day, he suffered from aphasia and right hemiplegia, and computed tomography (CT) showed left cerebral infarction due to left middle cerebral artery embolism. The emergent endovascular reperfusion was done, but mild subarachnoid hemorrhage occurred. The following day, TTE showed vegetations and aortic annular abscess, and MSSA was confirmed by blood culture. He was transferred to our institution for surgical treatment for IE. High fever continued, and inflammatory response was recurrent, because the infection was not under control. In addition, multiple systemic thromboembolisms were revealed by contrast-enhanced CT. He recovered to the level of moving his limbs slightly, but he could not speak. We did aortic homograft root replacement and coronary bypass grafting 6 days after the cerebral infarction. His postoperative course was uneventful and he was transferred to rehabilitation hospital on postoperative day 31. He reintegrated into society without neurological complications, and there are no recurrent infections and have been no structural valve deteriorations of the homograft in 5 years.