This report describes the case of a neonate with dextro-transposition of the great arteries and an intact ventricular septum who required postoperative extracorporeal membrane oxygenation support for an unexplained postoperative left ventricular dysfunction after an arterial switch operation. After surgery, a large aortopulmonary collateral suspected of causing overload to the left ventricle was diagnosed. Percutaneous embolization of the aortopulmonary collateral caused prompt improvement in patient's conditions and rapid weaning from mechanical ventilation support.