Amputation neuroma or traumatic neuroma is a tumor-like secondary hyperplasia that may develop after an accidental or surgical trauma. Amputation neuroma of the bile duct has occasionally been reported which occurred in the cystic duct stump late after the cholecystectomy. However, even if the amputation neuroma is suspected in a patient with late-onset jaundice after cholecystectomy, the differential diagnosis from a malignancy is difficult preoperatively. We experienced a case of the amputation neuroma of common bile duct (CBD) developed in a 70-year-old man who presented with a polypoid mass in CBD. He had undergone cholecystectomy 25 years ago and choledochojejunostomy 12 years ago, respectively. We have performed pylorus-preserving pancreatico-duodenectomy (PPPD) under the impression of CBD cancer. He had not been diagnosed of amputation neuroma until having undergone PPPD. We report a case of CBD neuroma mimicking CBD cancer, which was confirmed after PPPD.