Chylothorax in the neonatal period is a rare cause of respiratory distress. Surgical ligation of the thoracic duct is rarely necessary in congenital chylothorax. A 3 day-old newborn delivered by the cesarean section showed signs of respiratory distress suddenly and diagnosed as chylothorax on the right hemithorax. Conservative management such as multiple thoracenteses and tube thoracostomy drainage with nutritional support failed to close the leakage. At age of 60 days, we performed a supradiaphragmatic mass ligature of the thoracic duct visualized after injection of methylene blue into the thigh subcutaneously. Postoperatively, chylous effusion occurred in the left hemithorax and successfully treated with chest tube drainage for several days.