Liver transplantation (LT) is often viewed as the last resort for the treatment of congenital extrahepatic portosystemic shunt (CEPS) due to advancement of imaging and interventional radiology techniques. However, some patients still require LT, and criteria for LT are yet to be determined. We conducted a national survey of patients undergoing LT for CEPS between June 1998 and August 2018 and evaluated the clinical data and outcomes with a review of previously reported patients from the English-language medical literature. A total of 26 patients underwent LT in Japan at a median age of 5.2 years old. The most common indications for LT were persistent hyperammonemia (54%) and liver mass (50%), followed by pulmonary complications (38%). Pulmonary complications in all patients, including intrapulmonary shunt and pulmonary hypertension (PH), were improved after LT. Regarding the 29 previously reported patients in the English-language literature, a liver nodule (49%), including hepatoblastoma and hepatocellular carcinoma, was the most common indication for LT, followed by pulmonary complications (34%). A total of 25 (96%) patients in our survey and 26 (90%) patients in the literature review were alive with a median follow-up period of 9.5 and 1.6 years, respectively. Although LT has a limited role in management of CEPS, our study indicated that LT was safe as an alternative treatment for select patients with malignant tumor or pulmonary complications and those with complications related to new portosystemic collateral vessels after shunt closure, such as PH or hepatopulmonary syndrome.