A 77-year-old woman was referred to our hospital because of dilatation of the common bile duct. She had undertaken cholecystectomy for abdominal pain and abnormality of gallbladder 27 years before. Computed tomography (CT) and endoscopic ultrasonography (EUS) showed a tumor in the intrapancreatic bile duct and dilatation of the extrahepatic and intrahepatic bile ducts. Endoscopic retrograde cholangiopancreatography (ERCP) revealed a tumor in the intrapancreatic bile duct and pancreaticobiliary maljunction (PBM). Previous CT did not show dilatation of the bile duct, indicating that she had PBM without biliary dilatation. Biopsy of the tumor revealed adenocarcinoma, and she was diagnosed with distal cholangiocarcinoma. She undertook pancreatoduodenectomy. Pancreatography of the surgically resected specimen confirmed the connection between the main pancreatic duct and common bile duct. The final pathological diagnosis of the tumor was intrapancreatic papillary adenocarcinoma, pT2N0M0, stage IB. Recurrence has not been observed for 6 years after surgery. For PBM without bile duct dilatation, prophylactic cholecystectomy is recommended to prevent gallbladder carcinoma; however, biliary diversion surgery is controversial and is not generally recommended. Our case underscores that PBM without bile duct dilatation has a risk of extrahepatic biliary cancer and that careful follow-up is important after prophylactic cholecystectomy for a long period.