Basal cell adenocarcinoma is a rare salivary gland neoplasm. It is most commonly seen in the parotid gland, and its involvement in the minor salivary glands or upper respiratory tract is very rare. Surgical excision and/or radiotherapy are the mainstay treatment modalities. The nasopharynx is an unusual location for salivary gland basal cell adenocarcinoma. In this case report, the nasopharyngeal punch biopsy of a 60-year-old male patient was reported as salivary gland adenoma, but the final pathological diagnosis was changed to basal cell adenocarcinoma after endoscopic nasopharyngectomy. The clinical, radiological, and histopathological features of the case are presented in light of the literature. In addition, diagnostic clues are emphasized in cases of suspected non-epithelial tumors of the nasopharynx.