Systemic air embolism is a rarely reported complication of necrotizing enterocolitis in the neonatal population. It carries significant morbidity and mortality. We report a 6-day-old, term female neonate with a duct-dependent (systemic) congenital heart disease (interrupted aorta with patent ductus arteriosus and ventricular septal defect) who presented in extremis. The neonate was successfully resuscitated, mechanically ventilated, and put on intravenous prostaglandins in paediatric intensive care unit. She clinically improved but later she developed necrotizing enterocolitis which was complicated by systemic air embolism; both of which were identified by bedside ultrasound. Her condition deteriorated and she succumbed due to these complications.