Although branchial cleft cysts are common, papillary carcinomas arising from them are rare. Here we report a 41-year-old woman with papillary carcinoma originating from a right lateral branchial cleft cyst without any evidence of a papillary carcinoma in the thyroid gland. The patient underwent right lateral neck dissection followed by total thyroidectomy. We then confirmed papillary carcinoma arising from the branchial cleft cyst through microscopic and immunohistochemical staining with thyroglobulin (TG), thyroid-associated transcription factor-1 (TTF-1) and p63. It is the 10th case worldwide describing papillary carcinoma in a branchial cleft cyst with a review of the literature on the features of the disease and discussion of the role of immunohistochemical staining with TG, TTF -1 and p63. In conclusion, it should be emphasized that the surgeon must be cautioned of the possibility of primary papillary carcinoma in the branchial cleft cyst.