Aortopulmonary window is a rare congenital heart lesion. It might be associated with other CHDs, as well as with anomalous origin of the coronary arteries. Anomalous origin of the right coronary artery from the pulmonary artery (ARCAPA) is the most commonly described coronary artery anomaly in association with aortopulmonary window. We are describing a premature neonate who was diagnosed to have aortopulmonary window and ARCAPA immediately after birth, and had a successful operation at the age of 4 months. This report highlights the importance of very careful assessment of the coronary arteries in patients with aortopulmonary window.