Bronchogenic cysts are rare congenital malformation that need surgical removal. To date, bronchogenic cysts located in highest upper mediastinum excised by thoracoscopy have not been reported, though complete thoracoscopic extirpation of a bronchogenic cyst has been reported before. We excised two highest upper bronchogenic cysts by thoracoscopy successfully without any postoperative complication, demonstrating thoracoscopy could be a first-line therapeutic option even for highest upper mediastinum brochogenic cysts.