A 25-year-old unmarried woman with sex experience was referred to our hospital for the treatment of mild pneumothorax. On pneumothorax recurrence, thoracoscopy showed no cystic lesions on the visceral pleura but small defects and slightly elevated brownish multiple lesions on the diaphragm, leading to the presumed diagnosis of catamenial pneumothorax. The patient, therefore, underwent complete resection of the diaphragmatic lesions and extensive covering of the diaphragm using a polyglycolic acid sheet with 50 mL of autologous blood application. Post-operative pathological study showed that multiple endometrial tissues resided in the diaphragm. Central tendon with endometrial tissues, but not thick diaphragm with those, had diaphragmatic defects. Immunostaining showed that both endometrial cells and stromal cells were strongly positive for estrogen receptors. The patient later underwent surgery for exacerbated pelvic endometriosis for symptom relief but has been well without catamenial pneumothorax recurrence for 21 months. Thoracic surgeons should note that catamenial pneumothorax always presents mild to moderate pneumothorax and especially needs appropriate management of the diaphragmatic central tendon when surgically treating unmarried young women with catamenial pneumothorax.