Extrahepatic biliary duplication is a rare congenital biliary malformation, even more so when associated with heterotopic gastric mucosa. This case report highlights the difficulty of diagnosing such biliary abnormalities, in particular when the duplicated extrahepatic bile duct is the only structure visible by imaging as it is masking the common bile duct. This report shows that extrahepatic bile duct duplication may be a cause of chronic biliary obstruction and secondary sclerosing cholangitis. It has to be considered as a differential diagnosis of primary sclerosing cholangitis in children and adolescents. Furthermore, a potential link between the 46,XX karyotype and biliary duplication is discussed.