A 4-hour-old infant with profound cyanosis on an alprostadil infusion was urgently transferred to Rady Children’s Hospital with suspected CHD. Upon arrival, urgent echocardiography was performed but could not confirm the presence of discrete pulmonary veins or pulmonary venous drainage. Given the difficulty in delineating the anatomy, a cardiac CT scan was performed and demonstrated a nearly atretic common pulmonary vein with multiple small collaterals that drained to systemic veins. Due to the high risk of mortality associated with operative repair, the decision was made to proceed with compassionate withdrawal of care. The described anatomy of common pulmonary vein atresia remains rare, and to our knowledge, fewer than 40 cases have been reported in the literature. Albeit rare, common pulmonary vein atresia should be considered in the differential diagnosis of a severely cyanotic neonate.