Branchial cleft cysts are congenital anomalies arising due to incomplete involution of the branchial apparatus, most commonly involving the second cleft. They typically present as painless, cystic masses in the lateral neck with characteristic imaging features. However, atypical presentations in unusual anatomical locations can pose diagnostic challenges. We report the case of a 14-year-old female who presented with a painful swelling in the left upper neck. Ultrasonography and MRI revealed a heteroechoic, septated cystic lesion in the upper cervical region, deep to the parotid gland, with features overlapping multiple cystic neck pathologies. Differential diagnoses included lymphatic cyst, necrotic lymph node, cystic schwannoma, and salivary gland neoplasm. The lesion was aspirated and surgically excised. Histopathological examination confirmed the diagnosis of a second branchial cleft cyst, showing squamous epithelial lining with lymphoid aggregates and reactive lymphadenitis. This case highlights the diagnostic difficulty of branchial cleft cysts with atypical radiologic presentation, and underscores the critical role of radiology-pathology correlation in reaching a definitive diagnosis.