BACKGROUND: Neuroendocrine cancer is an extremely rare malignant tumor that originates from the nervous and the endocrine systems. This type of cancer can exist in almost any organ, although it is mainly found in the lung and gastrointestinal system according to current clinical reports. It is rarely found in the skull base, including primary and secondary neuroendocrine cancers. Therefore, diagnosis and treatment face a huge challenge. CASE DESCRIPTION: A 50-year-old female patient was introduced. She was admitted to the hospital due to persistent headaches, accompanied by nausea, vomiting, and decreased vision. Her case was primarily considered as a skull base malignant tumor based on clinical manifestations, imaging, and hormonal examinations. The patient then subsequently underwent neuroendoscopic surgery to remove the skull base tumor and repair cerebrospinal fluid leakage repair. The patient suffered from complications such as ghosting of the right eye after surgery, and she was given vitamin B1 orally. Pathological examination results show that the patient had neuroendocrine cancer (originated from sinus). We followed up the patient 2 months and 6 months after operation. At present, the patient recovered well, had no headache, and her spirit was significantly better than that before operation. CONCLUSIONS: Cranial neuroendocrine cancer has diverse clinical manifestations. CgA, Syn, Ki-67, CD56, and ACTH are important reference indicators for the diagnosis of neuroendocrine cancer. Neuroendoscopic transsphenoidal approach is a safe and effective surgical method.