Prosthetic valve endocarditis (PVE) can cause large cerebral vessel occlusion. Many reports suggested that mechanical thrombectomy (MT) is effective and useful for early diagnosis from the histopathological findings of thrombus. We present the case of a 62-year-old man, with a history of prosthetic aortic valve replacement and pulmonary vein isolation for his atrial fibrillation, who developed a high fever and an acute neurological deficit, with left hemiplegia and speech disorder. He was diagnosed as having an acute right middle cerebral artery embolism and underwent an MT. The embolic source was found to be a PVE vegetation. However, histopathological analysis of the thrombus could not detect the actual diagnosis. Although he was treated for bacterial endocarditis, his blood culture revealed a rare fungal infection with Exophiala dermatitidis not until >3 weeks after admission. Subsequently, a ß-D-glucan assay also indicated elevated levels. Although he underwent an aortic valve replacement on day 36, MRI showed multiple minor embolic strokes till that day. Early diagnosis of fungal endocarditis and detection of the causative pathogen are still challenging, and the disease has a high risk of occurrence of early and repeated embolic stroke. In addition to clinical findings and pathological studies, ß-D-glucan assay might be a good tool for the diagnosis and evaluation of fungal endocarditis.