A 65-day-old girl presented to the emergency room with lethargy, requiring emergency venoarterial extracorporeal membrane oxygenation for refractory cardiogenic shock. Initially, hypoplastic left heart syndrome was suspected. However, cor triatriatum with a pinpoint opening on the membrane was diagnosed based on a detailed echocardiographic examination. After membrane resection, the left heart size was restored. However, follow-up echocardiography performed 4 months later showed occlusion of both upper pulmonary veins and stenosis in both lower pulmonary veins. Hybrid balloon angioplasty was performed in all pulmonary veins, and stents were inserted into the right upper and lower pulmonary veins. Despite repeated balloon angioplasty, all pulmonary vein stenosis progressed over 6 months and the patient expired while waiting for a heart-lung transplant. Even after successful repair of cor triatriatum, short-term close follow-up is required for detecting the development of pulmonary vein stenosis.