Major abnormalities of pulmonary circulation are uncommon in the patient with pulmonary atresia and intact ventricular septum. Non-confluent pulmonary arteries have only rarely been described in this setting. In this case report, we describe a patient in whom the pulmonary arteries are non-confluent, with the right pulmonary artery supplied through a right-sided arterial duct, and the left pulmonary artery most likely through a fifth aortic arch, thus providing a systemic-to-pulmonary arterial connection. We discuss the various forms of non-confluent pulmonary arteries in the setting of pulmonary atresia and intact ventricular septum.