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A 63-year-old woman was admitted because of epigastric pain and obstructive jaundice. Endoscopic retrograde cholangiopancreatography and intraductal ultrasonography revealed a 25-mm papillary nodule in the middle to inferior portion of the common bile duct (CBD). Pancreaticobiliary maljunction (PBM) was also identified. Contrast-enhanced computed tomography also showed an enhanced nodule in the CBD, and we suspected intraductal papillary neoplasm of the bile duct. We performed pylorus-preserving pancreatoduodenectomy. Postoperative pathological examination revealed an inflammatory polyp in the middle CBD. Inflammatory polyp in the bile duct is rare and there are no previous reports accompanied by PBM. PBM is a major risk factor for biliary tract cancer. Preoperative diagnosis of a benign disorder was difficult in this case.