Chylothorax is a serious complication of congenital cardiac surgery and is significantly associated with increased morbidity and mortality. Central venous obstruction, which is often related to the insertion of central venous catheters for postoperative management, is known to be an important risk factor for treatment failure and mortality associated with this condition. We present the case of a 6-month-old girl with refractory chylothorax after surgical repair of tetralogy of Fallot. The chylous drainage continued for more than 2 months despite maximal conservative therapy (water restriction, total parenteral nutrition, and infusion of somatostatin and steroid) and surgical ligation of the thoracic duct. Subsequently, we observed stenosis of the superior vena cava (SVC) caused by large thrombi possibly associated with the prolonged use of central venous catheter placed in the internal jugular vein. Because transcatheter balloon dilation failed to relieve the stenosis, we performed stent implantation for the SVC and innominate vein. After the procedure, chylous drainage dramatically reduced, and the patient was discharged from the hospital. In conclusion, central venous obstruction due to thrombosis should be routinely examined when chylothorax is diagnosed and is resistant to conservative therapy after congenital heart surgery. Stent implantation can effectively relieve the venous obstruction and thus be a life-saving treatment option for this difficult condition.