Background The concept of mixed adenoneuroendocrine carcinoma (MANEC) was introduced in the 2010 World Health Organization classification of digestive neuroendocrine neoplasms. Bile duct invasion by MANEC is exceptionally rare. We herein report a case of MANEC with invasion of multiple bile ducts. Case presentation: A 60-year-old man presented with a 7-day history of upper abdominal pain, and a mass in the cystic duct was suspected based on computed tomography findings. The patient underwent resection of the extrahepatic bile ducts with concomitant radical lymphadenectomy and Roux-en-Y cholangiojejunostomy. Large cell neuroendocrine carcinoma was detected in a component of the resected tumor. According to the pathological and immunohistochemical features of the tumor, the final histopathological diagnosis was a biliary MANEC, tumor stage T2N0M1 (Stage IIIC). The patient recovered uneventfully and was discharged from the hospital 10 days after surgery. Conclusions We have described a rare case of extrahepatic MANEC invading multiple bile ducts, with particular emphasis on the physician’s awareness of MANEC and its optimal treatment. MANEC arising from extrahepatic bile ducts is rare, and surgical resection is the most effective treatment method.