Second branchial cleft cysts (BCCs) can occur anywhere from the tonsillar fossa to the supraclavicular area. Second BCCs usually lie on the great vessels of the neck, deep in the sternocleoidomastoid muscle or along its anterior border at the mandibular angle. Parapharyngeal second BCCs are an uncommon neoplasm and rarely extend to the skull base. We report the case of a 45-year-old male with symptoms of conductive hearing loss. Temporal bone CT scan showed effusion in the left middle ear cavity. Magnetic resonance imaging (MRI) revealed a cystic mass that was located at the left parapharyngeal space and eroded the skull table of the left temporal base. Excision of the lesion was achieved via a transzygomatic-transtemporal approach to the parapharyngeal space. Histopathological examination of the cyst wall showed a single layer of ciliated columnar epithelium without goblet cells or lymphoid tissue. The patient recovered without any complications and experienced complete resolution of left-sided hearing difficulty. We conclude the lateral transzygomatic-transtemporal approach allows surgeons direct access to the parapharyngeal space with satisfactory exposure for treating benign lesions of the parapharyngeal space.