Most amputation neuromas of the biliary tract occur in the cystic duct stump after cholecystectomy and are asymptomatic. However, when they arise in the main hepatic duct and are associated with obstructive jaundice, it is difficult to distinguish them from carcinoma. We describe a case in which preoperative differential diagnosis was difficult. A 60-year-old man was admitted to the Institute of Clinical Medicine, University of Tsukuba, with a chief complaint of jaundice. Cholangiography showed an irregularly elevated nodular lesion on the lateral wall of the common hepatic duct and multiple floating stones in the choledochus. Ultrasonography and computed tomography revealed one-sided regional thickening of the common hepatic duct associated with dilatation of the intrahepatic and extrahepatic bile ducts. Carbohydrate antigen 19-9 level was markedly elevated to 11,200 IU/mL in the bile juice, but was only 38 IU/mL in the serum, below the limit of abnormality. Cholangioscopy showed papillary tumor with coarse granular surface mimicking papillary carcinoma, but biopsy revealed no malignancy. The patient underwent hepaticocholedochus resection. Although the macroscopic finding from the surgical specimens was papillary carcinoma of the common hepatic duct penetrating to the hepatoduodenal ligament, histopathological examination revealed an amputation neuroma consisting of hypertrophic nerve tissues and giant cells containing foreign bodies, probably as a consequence of a previous cholecystectomy. The postoperative course was uneventful and the patient has been living well for the 5 years since the resection.