Cerebral thromboembolism is a rare but serious complication after Fontan operation. This is the report of a patient who underwent a successful intracardiac thrombectomy for cerebral thromboembolism after Fontan operation. A 2-year-old girl was referred to us with the diagnosis of tricuspid atresia without pulmonary stenosis, normally related great arteries, and a ventricular septal defect. Although she underwent a successful Fontan operation and division of the main pulmonary artery, she developed a cerebrovascular event at 3 weeks after the operation. Echocardiography demonstrated a large thrombus within the residue of the main pulmonary artery, and suggested that the thrombus had migrated into the systemic circulation by way of the ventricular septal defect. At 2 weeks after the cerebrovascular event, she underwent thrombectomy and excision of the pulmonary valve. Although she has developed slight left-sided hemiparesis, she is leading a normal life at 1 year after the operation.