We treated a 15-year-old patient with spontaneous pneumothorax associated with Swyer-James syndrome using video-assisted thoracoscopic surgery (VATS). Thoracic computed tomography showed hyperlucent areas in the bilateral lungs. Due to major air leakage continuing for a week, we conducted VATS bullectomy. Because the opposite lung suffered hypoplasia, intermittent bilateral pulmonary ventilation was required to sustain an adequate PaO2 in arterial blood gas analysis during surgery. Because of recurrent pneumothorax, we performed reoperation 10 months later, finding a few newly generated bullae. To the best of our knowledge, this is the first report of VATS used to treat a Swyer-James syndrome patient with pneumothorax.