Some studies link GERD and headaches, but their correlation still needs to be further investigated. One theory suggests that gastrointestinal disorders such as GERD increase the body’s sensitivity to pain. Studies show that the brain and stomach communicate through the central nervous system, endocrine system, and immune system. If there is any disturbance in the brain or gut, this can lead to a disruption in communication and lead to the development of headaches or even migraines.