A 17-year-old boy with homocystinuria was found to have a systolic murmur during a routine examination. Echocardiography demonstrated pulmonary hypertension (PH), and computer tomography angiography showed pulmonary thrombi. Although 12-month anticoagulation treatment reduced the thrombotic material within the main branch, it failed to clear thrombotic materials in the left and right lobar branches. Two years later, the patient was admitted to our hospital due to a worsening of PH. Treatment with bosentan, sildenafil and beraprost, in addition to anti-coagulant therapy, did not improve his PH. Balloon pulmonary angioplasty (BPA) was performed to remove the pulmonary thrombi. BPA markedly improved the patient's hemodynamics and exercise capacity. Close follow-up is scheduled to prevent any potential future thrombotic complications.