Primary branchiogenic carcinoma is a rare condition. In fact, most of the cases that were previously reported as such were actually cystic metastases of oropharyngeal carcinomas. We report a true case of primary branchial cleft cyst carcinoma. Our patient was a 42-year-old woman who presented with a painless fluctuant swelling in the right side of her neck. The lesion was completely excised, and pathology identified it as a squamous cell carcinoma in a branchial cleft cyst. Patients with this condition require a careful evaluation of the entire head and neck region, especially the oropharynx, to look for any cystic metastasis of the primary tumor.