We present a rare branchial cyst of the nasopharynx in a 57-year-old man. The cyst was located at the higher level between the roof and the left lateral band of the nasopharynx, and was removed by the endonasal approach following a preparatory septoplasty. While several cases of nasopharyngeal cysts have previously been reported, this appears to be the first case of the resection of such a cyst via the endonasal approach, and is a useful, and potentially less injurious, alternative to the transpalatal approach.