Background: Surgical ligation and endovascular embolization have been recommended for type II congenital extrahepatic portosystemic shunt (CEPS); however, no consensus has been reached. This study was designed to compare the safety and efficacy of surgical ligation and endovascular embolization for the treatment of type II CEPS. Methods: In this retrospective study, 23 consecutive patients diagnosed with type II CEPS between March 2011 and April 2019 were divided into either a surgical group (n=13; 41.5±19.9years) or the interventional group (n =10; 44.9±19.7years). The surgical group underwent laparoscopic surgical ligation of the shunt alone or ligation of the shunt and splenic artery and/or vein. The interventional group underwent endovascular embolization using microcoils, detachable coils and vascular plug. Results: All 23 patients received a one-step shunt closure, and their clinical symptoms were significantly improved within 3 months post-procedure and without recurrence during follow-up. The serum ammonia levels in both groups decreased after the procedure and dropped to normal level at 6 to 12 months post-procedure. Compared with baseline, the portal vein diameter in interventional group increased significantly at 3-, 6-, 12-, and 36-month post-occlusion (P=0.01 for all). The procedure time was shorter in interventional group (127.0±43.2minutes) than surgical group (219.8±56.7minutes; P <0.001). The intraoperative blood loss in interventional group (32.0±62.5mL) was less than that in surgical group (238.5±396.9mL; P=0.001).Conclusion: Both surgical ligation and endovascular embolization are effective in the treatment of type II CEPS. Endovascular embolization has the advantages of shorter procedure time, and less intraoperative blood loss. The ligation of the portosystemic shunt and splenic artery and vein is feasible with apparent safety, and it could avoid a second surgical treatment.