Branchial cleft anomalies represent a common cause of cervical mass in adults. Describing a case report, we reviewed embryology, clinical elements, and treatment options for parapharyngeal congenital cysts. A case of a parapharyngeal cyst mimicking a tonsillar abscess is presented. A second branchial cleft cyst was hypothesized on a clinical and radiologic basis and then confirmed by histologic data. Magnetic resonance imaging provided fundamental information for the study of the parapharyngeal mass and its relationship with surrounding structures. In literature, surgical excision is the recommended therapy. We removed the cyst through a transcervical approach, with no complications or recurrence after 3 years. In our opinion, cervicotomy should be considered the gold standard approach, even for lesions not palpable in the cervical area. When dealing with a parapharyngeal cyst, second branchial cleft anomalies should be considered. Our experience confirms that cervicotomy is a safe approach to parapharyngeal congenital lesions.