There are only a few case reports in which cholesterol crystals were found in the thrombus retrieved by mechanical thrombectomy for cryptogenic stroke, leading to a definitive diagnosis. We herein report a case of aortogenic embolic stroke diagnosed by the presence of rich cholesterol crystals in the retrieved thrombus and review the previously reported cases. A woman in her 80s was transferred as an emergency due to consciousness disturbance, right conjugate deviation, and severe left hemiparesis. Magnetic resonance imaging showed occlusion of the right middle cerebral artery (MCA) and acute infarction in the territory. The MCA was recanalized by thrombectomy using an aspiration catheter and stent retriever, and the symptoms improved. Although the physiological examination did not detect the embolic source during hospitalization, pathological examination of the thrombus revealed atheroma with numerous cholesterol crystal clefts and intermixing of fibrin. Contrast-enhanced computed tomography performed based on the pathological results showed atheromatous lesions in the aortic arch as the embolic source. As a subsequent treatment, medications of a strong statin and an antiplatelet agent were continued, and the patient had no recurrence. The finding that the retrieved thrombus is a simple atheroma containing cholesterol crystals with poor hemocytes suggests embolism due to plaque rupture. Pathological examination of the thrombus obtained by thrombectomy is one of the useful diagnostic approaches for stroke etiology and the determination of its treatment.