Branchial cleft cysts are congenital anomalies which develop in utero, most commonly arising from the second branchial cleft. They are often asymptomatic lateral neck masses but can enlarge and become symptomatic in the setting of infection. The cystic cavity can form a potential space which can harbor infection and, in rare cases, malignant spread of primary tumors. Herein, we present a rare case of a 28-year-old male with an enlarging branchial cleft cyst of six months duration following an upper respiratory infection. Routine post-surgical histopathological examination of the excised mass revealed metastatic papillary thyroid carcinoma. To our knowledge, this case is one of five cases reported within the primary literature. This case draws attention to the occult nature of papillary thyroid carcinoma and the importance of routine histopathological examination of seemingly benign surgically excised lesions.