Second branchial cleft cysts (BCCs) are the most common type of branchial abnormalities and usually found high in the neck. Oropharyngeal presence of a BCC is very rare. The authors report a rare case of oropharyngeal, second branchial, multilocular, cleft cyst in a 9-year-old child (8.0 × 5.0 cm in maximum diameter). The cyst was removed completely via extra/intraoral approach and did not have tract-like structure. The anatomic location together with the histopathology results, which showed a squamous epithelium-lined cystic wall with lymphoid aggregation, were characteristic findings of a BCC. Patient was discharged without any complication, and a regular follow-up of 6 months showed no evidence of recurrency. Having reviewed the literature, it seems to be that this is the first case to be reported of a multilocular BCC, excised of this size, from the oropharyngeal area in a child. Other pathological lumps of the neck have similar presentation with BCC, which makes it difficult, sometimes, to reach an accurate diagnosis. Clinicians should be aware of this pathology because it can be easily misdiagnosed as an odontogenic cyst and/or salivary gland infection, especially if it develops high up in the neck.