A 37-year-old female was admitted to our department because of sudden onset of left chest pain and dyspnea on the day before menstruation. She had a history of left-sided pneumothorax on two occasions. Her chest CT revealed left pneumothorax with multiple thin-wall cysts. She was diagnosed with spontaneous left-sided pneumothorax and was treated with continuous thoracic cavity drainage; however, her left-sided pneumothorax did not improve. In addition, it was complicated by right-sided pneumothorax. Therefore, she had surgery for her right-sided pneumothorax. Thoracoscopy revealed a cystic lesion in the right upper lobe and normal appearance of the diaphragm, and we performed partial resection of right upper lobe including the cystic lesion. Pathological examination of the pulmonary cystic lesion revealed endometriosis, and therefore we diagnosed her as having catamenial pneumothorax due to endometriosis. Radiologically, multiple pulmonary cysts due to endometriosis are rare in cases of catamenial pneumothorax. Catamenial pneumothorax should be considered in the differential diagnosis of patients with pneumothorax accompanied by multiple pulmonary cysts.