The exact cause of catamenial pneumothorax is unknown. Several different theories have been proposed involving metastatic, hormonal and anatomical abnormalities. It is possible that catamenial pneumothorax may have different causes in different cases.

In the metastatic model, catamenial pneumothorax is caused by the abnormal migration of endometrial tissue from the lining of the uterus (endometrium) to other areas of the body such as the diaphragm or the space in between the membranes lining the chest cavity wall and the lungs (pleural space). When endometrial tissue is found outside of the uterus, the term endometriosis is used. Many women with catamenial pneumothorax have endometriosis. Endometriosis can cause small holes or openings (fenestrations) in the diaphragm, which would allow air and fluid to pass through into the pleural space. Many women with catamenial pneumothorax have endometrial tissue in the lungs, a condition called thoracic endometriosis. However, some women with catamenial pneumothorax do not have diaphragmatic fenestrations or endometrial tissue in the lungs suggesting that other factors may play a role in the development of the disorder or that other causes of the disorder (apart from endometriosis) exist.

In the hormonal model, researchers believe that a hormone known as prostaglandin F2, which is elevated during ovulation, causes narrowing (constriction) of the small tubes within the lungs (bronchioles). Bronchiolar narrowing may cause the small air sacs (alveoli) of the lungs to rupture, allowing air to become trapped in the pleural space.

In the anatomical model, researchers believe that the absence of the cervical mucous plug, a normal occurrence during the menstrual cycle, allows air to pass from the genital tract into the pleural space through small holes or openings (fenestrations) in the diaphragm.

Another theory that has been proposed as a cause of catamenial pneumothorax is the spontaneous ruptures of blebs. Blebs are small blisters or pustules that may be filled with fluid or air and can develop on the lungs. Some researchers speculate that hormonal changes during the menstrual cycle may cause blebs to rupture, which in turn can result in pneumothorax.