Diagnosis and treatment for embolic stroke due to Infective Endocarditis (IE) is the challenging. We describe the case of acute middle cerebral artery occlusion with fever and inflammation underwent Mechanical Thrombectomy (MT) and retrieved atypical thrombus. That pathological finding, thrombus with bacterial colony, proved the diagnosis of IE. Following appropriate antibiotic therapy and replacement of the cardiac valve, the clinical outcome was favorable. Given this case experience and other reported cases, MT may be considered as a prime option for acute ischemic large-vessel occlusion due to IE.