Branchial cleft cysts are congenital anomalies of development, with the second branchial cleft cyst being the most common clinically. In extremely rare cases, branchial cleft cysts can undergo malignant transformation. Herein, we present a rare case of a 65-year-old male patient who had a painless neck mass on the left side for 6 months. Routine postoperative histopathological examination of the resected mass revealed branchial cleft carcinoma. We excluded the possibility of systemic metastasis through PET-CT and subsequently performed radical neck dissection. Routine follow-up revealed no recurrence after surgery. A PubMed search of the literature over the past 10 years yielded only 11 articles related to branchial cleft carcinoma. We hope this case will remind clinicians of the insidious nature of branchial cleft carcinoma and the importance of routine histopathological examination of seemingly benign surgical lesions.