Introduction: We aimed to retrospectively evaluate the use of acetaminophen, which may be a risk factor for the ductal canal, in the treatment of fever due to prostaglandin E1 (PGE1) infusion in newborns with critical congenital heart disease (CCHD). Methods: The study included newborns who were followed-up in our neonatal intensive care unit with the diagnosis of critical congenital heart disease, developed fever due to PGE1 infusion and had acetaminophen administered for antipyretic treatment. The patent ductus arteriosus diameters of the patients were evaluated by echocardiographic imaging before intravenous acetaminophen treatment and at the end of the day of acetaminophen treatment. Results: PGE1 fever was observed in 10 (6%) of 156 infants with ductus-dependent congenital heart disease. Intravenous acetaminophen treatment administered as an antipyretic in these infants did not cause the narrowing or closure of the ductal canal diameter, which would lead to clinical decompensation if it was closed, and the patients remained hemodynamically stable until surgery. Conclusions: It can be considered that controlled and rapidly administered intravenous acetaminophen therapy in the management of fever in neonates with congenital heart disease who develop fever as a side effect of high-dose intravenous PGE1 infusion therapy (≥0.3 mcg/kg/min) may prevent hemodynamic decompensation in these critically ill infants, and as a secondary outcome, it can be speculated that avoiding rapid daily increases in PGE1 maintenance infusion doses may be necessary to limit the number of paracetamol administrations in these infants.