An intramural coronary artery in the setting of truncus arteriosus (common arterial trunk) is an uncommon association. Following an uneventful surgical repair, a neonate developed a low cardiac output state deteriorating into cardiac arrest shortly after arrival into the intensive care unit, requiring extracorporeal membrane oxygenation support. Echocardiography and angiography showed occlusion of the left coronary artery, prompting emergency surgical reexploration. A "slit-like" orifice with an intramural left coronary artery was successfully unroofed, allowing full recovery. Full definition of the proximal coronary anatomy beyond the orifices should be investigated preoperatively in truncus arteriosus, as a missed intramural segment could lead to significant morbidity or mortality.