A high percentage of either retired or active military personnel who have served in the 1990-1991 Gulf War (GW1) suffer from chronic headaches and muscle and joint pain associated with a syndrome known as Gulf War Illness (GWI). Unfortunately, drug treatments for GWI-related headache and body pain has not shown to be effective and drugs such as morphine are habit-forming and contain long-term abusive side effects. Recently, the use of non-invasive brain stimulation such as repetitive transcranial magnetic stimulation (rTMS) has yielded favorable clinical outcome in depression and a few chronic pain conditions including headaches and body muscle pain. The treatment, which usually is non-painful and requires no anesthesia, utilizes a coil to non-invasively create a small current in a specific brain region for pain relief. The investigators have gathered preliminary outcome evidence supporting the use of the treatment in alleviating headache, joint and muscle pain, mood and sleep pattern in Gulf War Veterans with these chronic pain conditions. This 3-year study involving three Veterans Affairs (VA) sites (San Diego, Palo Alto, and Atlanta) aims to further validate the effect of rTMS in reducing GWI-related headache, muscle and joint pains, and other debilitating symptoms associated with mood, attention and sleep. While the study will be conducted at the VA, military personnel who are interested in study are welcome to participate in the study. Conducting the proposed multi-center will facilitate the clinical implantation of this non-invasive and non-drug therapy for reducing chronic pain symptoms and improving quality of life for both active and retired military personnel at both military and VA facilities.