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Neuroendocrine carcinoma (NEC) arising from the extrahepatic biliary tracts (EHBTs) is rare, and thus its management and prognosis remain poorly clarified. We herein describe a case of NEC in the perihilar EHBTs, and review the literature, together with a comparison between NECs in the perihilar and distal EHBTs, to elucidate the management strategy and oncological outcome of this rare entity.A 62-year-old Chinese male was admitted with complaints of painless jaundice. Imaging studies revealed a 2-cm mass in the hepatic hilum, regional lymph node involvement, and severe stenosis at the junction of the common hepatic ducts.The histopathological examination of the resected specimen demonstrated small tumor cells with round hperchromatic nuclei and scant cytoplasm. A detailed immunohistochemical analysis showed that the tumor was strongly positive for synaptophysin, CD56 and chromogranin A, with a Ki-67 labeling index greater than 80%. These results led to a diagnosis of NEC in the perihilar bile duct.The patient underwent surgical resection including a left hemihepatectomy, cholecystectomy, lymphadenectomy and Roux-en-Y hepaticojejunostomy.During the two months of follow-up, repeated imaging studies indicated tumor recurrence in the liver. The patient died 6 months after surgery.NEC in the EHBTs is extremely challenging to diagnose preoperatively because of mimicking other bile duct cancers. The prognosis of this disease entity is dismal, and most patients die within 2 years after diagnosis. Subtyping of NECs into perihilar NECs and distal NECs is beneficial for clinical applications, including guiding therapy selection and predicting survival.