An 86-year-old man was admitted for the abrupt onset of right hemiparesis and aphasia. DWI revealed the high intensity legion in the left insular cortex, and MRA demonstrated the left middle cerebral artery occlusion. Recanalization of the artery was not achieved after mechanical thrombectomy. The diagnosis of infective endocarditis was made as Enterococcus faecalis was cultured from the blood, and mobile vegetation was detected at the aortic valve by transthoracic echocardiography. The patient died from multiple organ failure at 19 days. Autopsy findings revealed fibrin-rich thrombus in the left middle cerebral artery containing neutrophils and bacteria. At the occluded site, neutrophils had intensively infiltrated into the vessel wall, and endothelial cells had partially disappeared. Moreover, disrupted internal elastic lamina was discovered. These findings could indicate that the thrombus had adhered to the vessel wall. The adhesion of the thrombus and vessel wall could be associated with unsuccessful recanalization after endovascular thrombectomy in patients with ischemic stroke due to infective endocarditis.