Isolated unilateral absence of the pulmonary artery without any intracardiac anomaly is a rare congenital cardiovascular disorder. We performed a successful anatomical repair after systemic-to-pulmonary shunt. The patient was a 1-day-old boy who was transferred to our institution because of continuous murmur. Cardiac echography revealed anomalous origin of the right pulmonary artery from the ascending aorta (AORPA). This aorto-right pulmonary arterial blood flow, however, disappeared in the following 2 days. We altered the diagnosis to right unilateral absence of pulmonary artery (UAPA) from AORPA. A right systemic-to-pulmonary shunt using a 3 mm polytetrafluoroethylene (PTFE) graft was placed, aiming for growth of the right pulmonary artery at the age of 8 days. Forty days after the initial surgery, he underwent a definitive procedure. The right pulmonary artery was anatomically reconstructed with an 8-mm PTFE graft. He was discharged in excellent condition on postoperative day 41. Cardiac catheterization, 1 year later, showed the surgically created right pulmonary artery was patent. A pulmonary perfusion scintigraphy showed satisfactory blood distribution in the right lung.