The optimal approach to patent ductus arteriosus management during systemic-to-pulmonary artery shunt placement is currently unknown. The purpose of this study is to examine the outcomes of variable strategies for patent ductus arteriosus management during Blalock-Taussig-Thomas shunt surgery. A retrospective cohort study of infants who underwent shunt placement was performed, comparing those who had the ductus ligated with those who had the ductus left open. Indicators of low cardiac output syndrome, development of necrotizing enterocolitis, and secondary outcomes such as resuscitation events were examined. Thirty-six infants were included all of whom had their shunt placed via median sternotomy. Twenty infants had their ductus ligated at the time of the shunt, and they were compared with 16 infants whose ductus was left open. There was no statistical difference in preoperative baseline characteristics, including corrected gestational age, age in days, weight, mechanical ventilation, vasoactive use, heterotaxy, and gastrointestinal anomalies. There was also no statistical difference in postoperative indicators of low cardiac output, including urine production, total fluids given, renal injury, maximum lactate, and vasoactive-inotropic score. Three patients had postoperative renal injury, and all were in the ligated duct group. There was also no statistical difference in any secondary outcomes, including the development of necrotizing eneterocolitis, resuscitation events, reinterventions, length of intubation, total length of stay, and mortality. This study provides evidence that variable management of the ductus during shunt placement does not significantly impact outcomes. Leaving the ductus open allows for a potential rescue source of pulmonary blood flow and does not appear to increase the risk of postoperative low cardiac output.