Klippel-Trenaunay syndrome is a rare congenital mesodermal abnormality characterized by varicose veins, cutaneous hemangiomas, soft tissue and bony hypertrophy of limb. Potential complications such as deep venous thrombosis and pulmonary thromboembolism have not been reported in Korea to date. We demonstrate the case of a 48-year-old woman with Klippel-Trenaunay syndrome with extensive varicose veins on right lower limb, hypertrophy of left big toe and basilar artery tip aneurysm, complicated with acute submassive pulmonary thromboembolism treated successfully with intravenous thrombolytic therapy.