Hypoplastic left heart syndrome in association with an anomalous origin of a coronary artery from the pulmonary artery is a very rare congenital malformation. In the few reported cases, the left coronary artery or the circumflex artery arises from the right pulmonary artery. We describe a newborn who presented with hypoplastic left heart syndrome, and at the time of operation had an anomalous origin of the right coronary artery from the right pulmonary artery that was detected. The patient underwent a successful modified Norwood procedure with direct reimplantation of the right coronary artery to the neo-aorta.