Branchial cleft squamous cell carcinoma is extremely rare, compared to the far more frequent cystic metastastic cervical lymph nodes arising from primary malignancies. This was a 40-year-old man presenting with a well-defined, two-month history of a slowly-growing lateral neck mass. He underwent complete tumor excision. The pathological diagnosis was squamous cell carcinoma originating from a branchial cleft cyst, which was characterized histologically by an epithelial-lined cyst with dysplasia to in situ carcinoma transitional zone.