Rationale: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.Patient concerns: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.Diagnoses: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.Interventions:The patient underwent surgical resection including a left hemihepatectomy, cholecystectomy, lymphadenectomy and Roux-en-Y hepaticojejunostomy.Outcomes:During the two months of follow-up, repeated imaging studies indicated tumor recurrence in the liver. The patient died 6 months after surgery.Lessons: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.