We report a patient with apical hypertrophic cardiomyopahty (AHCM) complicated by a cardiogenic cerebral embolism. A 56-year-old man was admitted to our hospital because of a transient ischemic attack. He had been diagnosed as having AHCM at the age of 39 years. The intravenous administration of heparin was immediately started; however, he developed a weakness in his right fingers on the second day. A brain MRI examination showed multiple small infarctions in the cortex of the left frontal and temporal lobes. Transthoracic echocardiography revealed the hypokinetic movement of the myocardium and a thrombus in the apex. We suspected that the hypertrophic apex had become dilated, causing the formation of the thrombus. He then developed a cardiogenic cerebral embolism. The thrombus in the apex disappeared after the continuous administration of heparin intravenously. Here, we emphasize that patients with AHCM in the dilatation phase must receive warfarin therapy to prevent cardiogenic cerebral embolism.