We encountered a rare case of a well-differentiated endocrine carcinoma originating from the bile duct in association with a congenital choledochal cyst (CCC). The patient is a 28-year-old woman referred to our clinic for pruritus. Laboratory data showed mild elevation of serum hepatobiliary enzymes. Computed tomography and magnetic resonance imaging demonstrated pancreatobiliary maljunction and a Todani type IV-A CCC from the inferior bile duct to the bilateral intrahepatic bile ducts. A solid tumor was detected in the middle portion of the common bile duct. Pancreatoduodenectomy and total extrahepatic bile duct resection was performed. Based on pathologic and immunohistochemical examinations, a diagnosis of well-differentiated endocrine carcinoma was made according to the World Health Organization criteria. To our knowledge, this is the third report of a neuroendocrine tumor originating from the bile duct in association with a CCC.