Premature closure of the ductus arteriosus (PCDA) and transposition of the great arteries (TGA) cause persistent pulmonary hypertension of the newborn (PPHN). We present a case of a newborn who demonstrated d-TGA with ventricular septal defect (VSD) and pulmonary stenosis (PS) complicated by PCDA. The neonate showed severe cyanosis resistant to resuscitation soon after birth, and was diagnosed with d-TGA with VSD by echocardiography. PPHN was also suspected based on physical symptoms and results of echocardiography. The neonate was given inhaled nitric oxide, prostaglandin E1, and catecholamines under sedation, and underwent a balloon atrial septostomy (BAS). His condition gradually improved, and he was extubated on day 7, but his pulmonary subvalvular stenosis gradually worsened and pulmonary blood flow was markedly decreased. A second BAS was performed on day 27 and he showed no improvement. Blalock-Taussig shunt surgery was performed on day 34, which markedly improved his condition. The co-existence of d-TGA and PCDA is generally a lethal state. In our patient, an increase in pulmonary blood flow during the fetal period was restricted because of PS and outlet flow from the left ventricle to the right ventricle via the VSD. This restricted blood flow through the ductus arteriosus, which led to narrowing of the DA. At the same time, damage to and constrictive changes of the pulmonary vessels were prevented. The ductus arteriosus should be carefully evaluated to exclude PCDA in cases of d-TGA. The presence of both VSD and PS may be a prognostic factor in such cases.