A 16-year-old girl developed dyspnea 9 years after surgery for patent ductus arteriosus with pulmonary hypertension (pulmonary to systemic peak systolic pressure ratio; Pp/Ps 1.0). The postoperative course had been uneventful with a decreased Pp/Ps. It was revealed this time, however, that the pulmonary arterial pressure again elevated to be 186/133 mmHg (Pp/Ps 1.90). Postoperative progression of pulmonary angiopathy was first suspected. Whereas, the findings with pulmonary perfusion scintigraphy and arteriography were remarkably different between the right and left lungs, suggesting that the progression of pulmonary hypertension was not caused by that of pulmonary angiopathy but by the association of thromboembolism in small pulmonary arteries. The patient succumbed to intractable cardiopulmonary failure, strongly appealing for the necessity of organ-transplantation therapy in Japan. This case also indicated the particular importance of a close follow-up of the cases with pulmonary hypertension remaining after corrective surgery.