A 28-year-old male was referred to our hospital with dyspnea. He was diagnosed as having chronic thromboembolic pulmonary hypertension, and a pulmonary endarterectomy (PEA) was performed. However, exertional dyspnea remained because of residual pulmonary hypertension; therefore, the patient was re-admitted to our hospital 1 year after PEA. We performed computed tomography and pulmonary angiography and found web and band lesions in the distal pulmonary artery with a high pulmonary artery pressure. Although further management was complicated because the patient had an anaphylactic shock to iodine-based contrast media, we eventually completed five sessions of balloon pulmonary angioplasty (BPA) using gadolinium contrast medium. His symptoms and hemodynamics dramatically improved after a series of BPA. After 15 months, mean pulmonary arterial pressure reduced from 67 mmHg to 20 mmHg, and subjective symptoms improved from stage Ⅳ to I as per the WHO classification system. BPA is a potential procedure for residual pulmonary hypertension after PEA and could be safely performed using gadolinium contrast medium for patients with iodine allergy.