To review the current institutional practice to treat patients with congenital extrahepatic portosystemic shunt (CEPS) and to determine the optimal strategy. We retrospectively reviewed the records of 55 patients diagnosed with CEPS at our center between December 2008 and March 2022. Among these 55 patients, 44 (80.0%) received treatment for CEPS at a median age of 4.7years. The most common indication for treatment was cardiopulmonary complications (45.5%). Therapeutic intervention included shunt closure by endovascular techniques (50.0%) or surgery (40.9%), and liver transplantation (9.1%). A total of 11 were classified as short shunt types, and surgical ligation was performed in all to preserve the major vascular system and prevent complications (p<0.001). Children who received a surgical ligation were more likely to develop complications after shunt closure (p=0.02). Among seven patients with portopulmonary hypertension (POPH), one patient, who received a shunt ligation at <1year-of-age, was only able to completely discontinue medication. Most other CEPS-related complications were completely resolved. Post-treatment complications, including thrombosis and symptoms of portal hypertension, were seen in 16 patients. After shunt closure, one patient was scheduled to undergo liver transplantation for progressive POPH and large residual hepatocellular adenoma. During follow-up, one patient without any treatment for CEPS developed POPH 16years from the diagnosis. Earlier therapeutic interventions should be strongly considered for patients with POPH related to CEPS. However, in view of the invasiveness and treatment complications, special attention should be paid to the management of patients with short shunt types.