A 48-year-old male visited the emergency room suffering from acute dysarthria and right hemiplegia. Brain magnetic resonance imaging (MRI) revealed multiple cerebral infarctions. Echocardiography showed a mass in the left atrium. He was diagnosed with cerebral embolism due to left atrial myxoma. Open heart surgery immediately after the attack is generally considered contraindicated because of such problems as hemorrhagic infarction or brain edema. However, relapse of embolism may make the condition worse and miss the timing of surgery. Eventually, we electively performed excision of the myxoma 20 days after the onset of cerebral infarction. The postoperative course was uneventful. This is a report about a rare case of open heart surgery shortly after the attack. The indication and the appropriate timing of open heart surgery following cerebral embolism were discussed.