Extrahepatic portosystemic shunts, known as Abernethy malformations, were first reported by John Abernethy in 1793. They are classified into two types: Type I refers to a congenital absence of the portal vein and Type II refers to a shunt involving a side-to-side anastomosis with reduced portal blood flow into the liver parenchyma. This malformation is so rare that less than 100 cases have been reported in the medical literature. We report the case of a 13-month-old boy who had a congenital extrahepatic portocaval shunt with a hypoplastic portal vein. This case was complicated with an atrial septal defect and a large hyperplastic nodule in the liver. The patient was diagnosed with a Type II Abernethy malformation. We planned on surgical occlusion of the extrahepatic portocaval shunt. However, six months later, the patient had a sudden onset of a fever of unknown origin and developed hepatic encephalopathy. Although he underwent a liver transplantation, he died of acute hepatic failure.