Branchial cleft cysts, arising from developmental anomalies of the branchial apparatus, represent a rare entity in adult populations. This case report presents a unique instance of a 32-year-old female with a second branchial cleft cyst prominently involving the great auricular nerve, an undocumented finding in the existing literature. The patient initially presented with progressive left-sided neck swelling, accompanied by localized pain radiating to the auricle and headaches, without systemic symptoms. Diagnostic imaging confirmed a cystic mass adjacent to vital neck structures, necessitating surgical intervention. Histopathological analysis post-excision confirmed typical features of a benign branchial cyst. The postoperative course was uneventful, with complete resolution of symptoms upon follow-up. This case capitalizes the diagnostic challenges and therapeutic considerations in managing branchial cleft cysts, particularly highlighting the exceptional involvement of the great auricular nerve. Further research is warranted to elucidate the pathogenesis and optimal management strategies for such atypical presentations.