Branchial cleft cysts are uncommon malformations that result from various degrees of incomplete closure of branchial apparatus during embryologic development. Clinical presentation of these lesions can be cystic and/or fistula formation on the head and neck region. Nasopharyngeal region is one of the unexpected anatomical sites of these malformations, and definite diagnosis was only disclosed by histopathologic examination of the specimen. The common presenting symptoms are one sided or bilateral nasal obstruction and one-sided otitis media with effusion. In this paper, we presented a nasopharyngeal branchial cleft cyst with a presenting symptom of bilateral otitis media with effusion. According to the best of our knowledge, this is the first case of bilateral otitis media with effusion due to a nasopharyngeal branchial cleft cyst, which is a very rare malformation.