Background: We present a rare case of a 12-year-old male child with seizures, chest pain, fever, cough, and breathing difficulty, revealing a large cystic lesion in the left paratracheal chest region. Coexisting tubercular lesions in the brain complicated the diagnosis. The patient had been under anti-tubercular treatment prior to admission. Case Report: A Video-assisted Thoracoscopic Surgery (VATS) was performed, excising the 8×7 cm cyst causing partial collapse of the left upper lobe lung. The cyst, intricately connected to the tracheal wall and vascularized by the left subclavian artery, was meticulously dissected, aspirated, and removed. Post-surgery, the patient recovered well, with the chest tube removed on the second day. Follow-up imaging confirmed lung expansion, and the patient was discharged on the third post-operative day. Conclusion: VATS proved to be an effective and minimally invasive technique for the excision of a large bronchogenic cyst, ensuring a rapid recovery and excellent long-term outcomes. This case highlights the significance of multidisciplinary approaches and precise surgical techniques in managing such intricate cases in young patients.