Nasopharyngeal branchial cysts present laterally as well as ascend from the fossa of Rosenmuller and trace superiorly inside the bony immures of the pharyngotympanic tube. Other commonly related disease conditions with respect to nasopharyngeal cyst include the Rathke’s pouch cyst, Thornwaldt cyst from the pharyngeal bursa along with the branchial cleft cyst. Here in our study, we report a case of a 25-year-old male presented with symptoms of snoring for the past 2 years. On zero-degree endoscopic examination, a nasopharyngeal mass was seen arising from the lateral wall of the nasopharynx extending to the oropharynx. Further based on his radiological investigations, a localized non-enhancing nasopharyngeal cystic mass was seen extending from the left lateral wall of nasopharynx to oropharynx and was diagnosed as nasopharyngeal cyst. Thus, the surgical removal of the nasopharyngeal cyst has been performed through a transoral endoscopic technique with no remnants at the surgical site. The histopathological findings revealed stratified squamous epithelium with subepithelial infiltration of lymphoid follicles, thus confirming the diagnosis as branchial cleft cyst. The patient was discharged with no complications and have been periodically advised for a follow-up. Conclusively, the cyst of 2nd branchiogenic origin in the nasopharynx is extremely sporadic and till date, only a small number of cases have been reported.