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Purpose: To assess the long-term results after Rex bypass (RB) shunt and Rex transposition (RT) shunt and determine the optimal approach., Methods: Between 2010 and 2019, traditional RB shunt was performed in 24 patients, and modified RT shunt was performed in 23 children with extrahepatic portal hypertension (pHTN). A retrospective study was conducted based on comparative symptoms, platelet counts, color Doppler ultrasonography and computed tomographic portography of the portal system, and gastroscopic gastroesophageal varices postoperatively. The portal venous pressure was evaluated intraoperatively., Results: The operation in the RB group was notably more time-consuming than that in the RT group (P < 0.05). Compared to RT shunt, the reduction in gastroesophageal varix grading, the increases in platelets, and the caliber of the bypass were greater in the RB group (P < 0.05). Although not statistically significant, higher morbidity of surgical complications was found after RT shunt (17.4%) compared with RB shunt (8.3%) with patency rates of 82.6 and 91.7%, respectively. Additionally, patients exhibited a lower rate of rebleeding under the RB procedure (12.5%) than under the RT procedure (21.7%)., Conclusions: The RT procedure is an alternative option for the treatment of pediatric extrahepatic pHTN, and RB shunt is the preferred procedure in our center.