Certain congenital heart diseases (CHD) may be difficult to diagnose when associated with poor precordial window or concurrent critical condition. We report a case of supracardiac type TAPVR with obstruction, of which the initial diagnosis was meconium aspiration syndrome (MAS) complicated with persistent pulmonary hypertension of the newborn (PPHN). The patient's critical condition required extracorporeal membrane oxygenation (ECMO) support, and the diagnosis of TAPVR was made incidentally when an open heart surgery was required to remove a thrombi in the aortic arch. The patient recovered well after a rerouting surgery of TAPVR. The possibility of making an earlier diagnosis from clinical signs, reversed differential cyanosis and high oxygenated blood in the superior vena cava (SVC) is further explained.