Anomalous origin of the right coronary artery from the pulmonary artery (ARCAPA) is a rare congenital defect, and few cases have been reported in the pediatric age group. Unlike the anomalous origin of the left coronary artery from the pulmonary artery (ALCAPA), patients with ARCAPA are usually asymptomatic and often diagnosed incidentally. Here, we present a surgical case of a 2-month-old male who was suspected of having ARCAPA in the neonatal period. The patient was suspected of having ARCAPA due to the detection of a heart murmur and the results from an echocardiogram taken the 4th day after birth. Coronary angiography on the 37th day after birth showed the contrast flow to the pulmonary artery through the right coronary artery from the left coronary artery; thus, we diagnosed ARCAPA. Surgical intervention should be performed before the appearance of myocardial ischemia due to decreasing pulmonary artery pressure, so we performed reimplantation of the right coronary artery to the ascending aorta and patch plasty of the pulmonary artery at 2 months after birth. The patient was discharged from the hospital on the 16th day after the operation, and a 6-month postoperative coronary angiography revealed good right coronary flow and the disappearance of collaterals.