We report a rare case of carcinoma of the cystic duct (CCD) associated with pancreaticobiliary maljunction (PBM). A 63-year-old man had presented with relapsing cholecystitis of 4 months, duration. Computed tomography showed a distended gallbladder: however, small mass in the cystic duct was overlooked. Endoscopic retrograde cholangiopancreatography demonstrated a long common channel (20-mm-long) and fusiform dilatation of the common bile duct, findings, which were consistent with PBM. At laparotomy, we found a papillary tumor, 20 mm in diameter, that obstructed the cystic duct. The patient underwent resection of the gallbladder and the common bile duct, lymph node dissection in the hepatoduodenal ligament, and hepaticojejunostomy. Histologic study revealed a papillary adenocarcinoma confined within the subserosal space. There was no lymphatic or perineural invasion of cancer cells. The surrounding cystic ductal mucosa showed dysplasia and hyperplasia, and the gallbladder and common bile duct showed severe inflammation. The patient has been doing well for 16 months after surgery, without tumor recurrence. This case suggests a relationship between CCD and chronic biliary inflammation caused by PBM, as in cases of gallbladder carcinoma.