A 78-year-old male patient came to our hospital with a chief complaint of fever. Computed tomography revealed an indistinct tumor in the pancreatic head, along with dilatation of the bile duct and main pancreatic duct. An endoscopic transpapillary biopsy demonstrated adenocarcinoma in the glandular epithelium and a dense formation of quasi-round cells. Pathology results indicated positive CK AE1/AE3 and INSM-1, negative CD45, and a Ki67 index of about 80%, leading to a diagnosis of neuroendocrine carcinoma (NEC) Grade 3 of the pancreatic head. Consequently, a pancreatoduodenectomy was performed. Postoperative pathology revealed small cell NEC (SCNEC) at the pancreatic head, with infiltrative growth of atypical gland ducts around the bile ducts, indicating the presence of a well-differentiated adenocarcinoma. The adenocarcinoma contained in situ lesions and biliary intraepithelial neoplasia (BilIN), with SCNEC being contiguous. Therefore, the diagnosis was NEC originating from the extrahepatic bile duct, which invaded the pancreatic head. NEC of the extrahepatic bile duct is rare, accounting for approximately 0.2-2% of gastrointestinal neuroendocrine tumors, and it has a poor prognosis, similar to other gastrointestinal NECs, even when surgical treatment is performed. The patient remained an outpatient without recurrence 17 months postoperatively.