Primary liver tumours in neonates with single-ventricle palliation are exceedingly rare. We present the first reported case of neonatal hepatoblastoma with severe Ebstein’s anomaly following Starnes procedure. The patient’s postoperative course highlights the challenges and complications in simultaneous management of these diagnoses. Transition from shunted single-ventricle physiology to bidirectional cavopulmonary connection improved end-organ function, permitting more aggressive hepatic malignancy treatment.