Severe hyperammonemia (hyperNH3) in neonatal cardiac failure after cardiac surgery is rare. We report a case of a 2470-g female infant born at the week 37 of gestation with complex congenital heart disease (truncus arteriosus type III, interrupted aortic arch and tricuspid valve insufficiency) and hemodynamically non-significant intrahepatic arterio-venous malformation. She developed hyperNH3 (highest NH3 blood level: 467 µmol/L) without severe liver failure (INR of 1.9). The origin of the hyperNH3 was multifactorial including limited capacity of liver detoxification function due to congenital porto-caval shunt, liver ischemia, excessive protein intake and increased protein catabolic rate. HyperNH3 treatment partially succeeded in decreasing ammonia level and included discontinuation of protein intake, administration of phenylacetate and sodium benzoate. This case highlights the fact that NH3 detoxification by the liver has limitations for a neonate with multifactorial causes that decrease liver perfusion.