The existence of primary branchiogenic carcinoma is controversial. In 1950, Martin et al. established four criteria for the diagnosis of primary branchiogenic carcinoma. In 1989, Khafif et al. proposed new modified criteria, which are currently most recognized in the literature. A 54-year-old woman presented the well-defined, fluctuant, painless mass on her left neck and underwent a complete excision under the clinical diagnosis of the branchial cleft cyst. The initial pathological impression was a branchiogenic squamous cell carcinoma. However, it did not coincide with a true primary branchiogenic carcinoma clinically. After the guided biopsy of suspicious areas found a squamous cell carcinoma of the tongue base, the patient was treated by combination chemotherapy with radiotherapy. Thus, we report this case with a review of the literature.