We report a case of double cancer of the cystic duct and gallbladder associated with low junction of the cystic duct. A 73-year-old woman was admitted to the hospital complaining of upper abdominal pain. Endoscopic retrograde cholangiography showed a stenotic lesion in the lower common bile duct and no visualization of the cystic duct or gallbladder. Enhanced computed tomography revealed a heterogeneously enhanced tumorous lesion around the lower bile duct in the pancreatic head. A diagnosis of cancer arising from the cystic duct that entered the lower part of the common hepatic duct was made by intraductal ultrasonography, which showed an intraluminal protruding lesion in the cystic duct. Isolated gallbladder cancer was also diagnosed, by abdominal computed tomography. She underwent pancreaticoduodenectomy with dissection of regional lymph nodes. Histological examination revealed moderately differentiated adenocarcinoma of the cystic duct and well-differentiated adenocarcinoma of the gallbladder. Double cancer of the cystic duct and gallbladder is extremely rare, and this case also suggests a relationship between a low junction of the cystic duct and neoplasm in the biliary tract.