We report a case of double cancer of the gallbladder and the common bile duct associated with anomalous junction of the pancreaticobiliary ductal system, and review the literature of similar case reports. A 66-year-old woman was admitted to an associated hospital complaining of upper abdominal pain, and was diagnosed as having pancreatitis. Abdominal imaging revealed an irregularly protruding mass at the body of the gallbladder and an intraluminal protrusion at the lower third of the common bile duct. Endoscopic retrograde cholangiopancreatography also revealed anomalous junction of the pancreaticobiliary ductal system with congenital biliary dilatation of 14 mm in the largest diameter. She underwent surgical resection of the gallbladder, the extrahepatic bile duct and the gallbladder bed of the liver with a dissection of the regional lymph nodes for double cancer of the gallbladder and the bile duct associated with anomalous junction of the pancreaticobiliary ductal system. She is still alive 33 months after surgery without any signs of recurrence. There were 12 patients (including our case) reported in the literature who had double cancer of the gallbladder and the extrahepatic bile duct associated with anomalous junction of the pancreaticobiliary ductal system. Only 33% of these 12 patients had jaundice. Tumors of the 12 patients were commonly early-stage cancer both in the gallbladder (36%) and in the extrahepatic bile duct (73%). Therefore, we concluded that precise preoperative imaging of the total biliary tract should be required in order to detect early-stage cancer in patients with anomalous junction of the pancreaticobiliary ductal system before planning surgical procedures, and consideration should be given to the possibility of multiple occurrences of biliary tract cancers.