Development of an invasive squamous cell carcinoma within a branchial cleft cyst (branchiogenic carcinoma) is very rare and this case is the first description of cytologic findings in Korea. A 62-year-old man presented with a 5-month history of an enlarged right neck mass. Fine needle aspiration cytology of the mass showed low cellularity and the background containing proteinaceous debris, inflammatory cells, and histiocytes suggested a cystic nature. Abundant lymphocytes, a few anucleated squames, and rare atypical squamous cells with pyknotic nuclei and abnormal keratinization were also noted. After excision of the mass, histologic findings were consistent with a branchiogenic carcinoma. We recommend to raise the possibility of carcinoma (primary or metastatic) when we observe a few dyskeratotic cells in a cystic mass within the neck area, especially in an old male.