Chylothorax is a critical complication after surgery for congenital heart disease, which markedly compromises the postoperative course with increased mortality. As the cardiovascular load additively causes stagnation of the thoracic duct, chylothorax after palliative cardiac surgery can be highly refractory to the therapies. Here we report a case of two patients with refractory chylothorax attributed to hemodynamic load which was successfully treated with minocycline pleurodesis. In combination with congenital heart disease, extremely low birth weight coupled with prematurity in case 1 and venous obstruction with excessive volume load due to additional aortopulmonary shunt in case 2 additively increased resistance to the therapies, including fasting with total parenteral nutrition (TPN), XIII factor supplementation, octreotide infusion, as well as the use of steroids. As pleural effusion was sustained at more than 50 ml/kg/day, the condition of both patients deteriorated severely; pleurodesis using minocycline was urgently introduced. Pleural effusion declined at every session and both cases were in remission in a few sessions without unfavorable acute reaction. No symptoms suspecting chronic adverse effects were observed during follow-up, including respiratory dysfunction, pulmonary hypertension, tooth staining, or abnormal bone mineralization. Although the application of minocycline for children should be minimized, minocycline pleurodesis can be an option for patients with refractory and life-threatening chylothorax.