Second branchial cleft cysts are usually present as a fluctuant neck mass along the anterior border of the sternocleidomastoid muscle. When they are found in this typical location, accurate diagnosis on initial presentation is not difficult. Parapharyngeal presence of the branchial cleft cyst is very rare. We report a case of second branchial cleft cyst presenting as a parapharyngeal cystic mass in 51-year-old male. Before coming to our clinic, the patient had been diagnosed as parapharyngeal abscess, resulting in several attempts at removal. However, symptoms and parapharyngeal abscess recurred. We performed complete surgical resection of the parapharyngeal cystic mass via transoral approach only with oropharyngeal incision. The cystic mass was located in the parapharyngeal space and did not have tract-like structure. Histopathologic examination confirmed that the excised cyst was branchial cleft cyst. Patient discharged without any surgical complication and there was no evidence of recurrence for 2 years follow-up.