Malposition of the branch pulmonary arteries (MBPA) is an unusual malformation characterised by anomalous origin of both pulmonary arteries from the main pulmonary trunk. To date, only few cases have been reported. Herein, we present the first case report of a 3-day-old, full-term male neonate with the lesser form of crossed pulmonary arteries in Saudi Arabia detected by echocardiography and confirmed by cardiac CT. Crossed pulmonary arteries is not a rare anomaly, but it is a somewhat underreported anomaly, and their recognition is important because it is usually associated with other CHDs, airway obstruction, extra-cardiac anomalies, and certain genetic syndromes.