Medical therapy for chronic pulmonary thromboembolism is limited, and surgical treatment has become more frequent recently. We have performed pulmonary thromboendarterectomy on a patient with chronic pulmonary thromboembolism accompanied by protein C deficiency. The patient was a woman aged 68 years who had protein C deficiency. The preoperative condition was New York Heart Association functional class IV. Hypoxemia, marked pulmonary hypertension, and low cardiac output were observed. After a median sternotomy, moderate hypothermia was induced using a cardiopulmonary bypass, and thromboendarterectomy in the pulmonary artery was performed. The arterial blood oxygen concentration improved, and the mean pulmonary pressure decreased. The cardiac output also increased, and New York Heart Association functional class improved to I. Pulmonary thromboendarterectomy under cardiopulmonary bypass was effective for chronic pulmonary thromboembolism accompanied by protein C deficiency.