This case report describes a male neonate with Graves' disease. The mother's pregnancy was complicated by poorly controlled Graves' disease. The neonate was diagnosed with thyroxine (T3)-predominant Graves' disease with low free triiodothyronine (T4) and high free T3 during antithyroid drug therapy. The patient also presented with persistent pulmonary hypertension of the newborn due to hyperthyroidism and airway stenosis caused by goiter. It was difficult to control thyroid function and maintain free T4 levels with inorganic iodine, thiamazole, and levothyroxine sodium hydrate. We successfully controlled thyroid function using the previous treatments in combination with propylthiouracil. Propylthiouracil suppresses type 1 iodothyronine deiodinase, and its pharmacological action suppresses the conversion of T4 to T3. Therefore, we used propylthiouracil at an earlier stage of intervention in this case. We ceased administration of antithyroid drugs on day 85 of life. Subsequently, as the TRH loading test revealed central hypothyroidism, oral administration of levothyroxine sodium hydrate was continued. Its administration was discontinued at the age of 1 yr. Thyroid-stimulating hormone recovered to normal values, and his development had progressed without complications by the age of 2 yr.