Abstract Persistent headache is one of the most common debilitating symptoms in military personnel suffering from mild traumatic brain injury (MTBI). Along with headaches, these patients also suffer from associated mood and attentional deficit. Conventional analgesics have not been shown to be effective in managing these debilitating symptoms and consist of untoward side effects and abusive complication. Our preliminary study indicates a week long course of non-invasive central neuromodulation method called repetitive transcranial magnetic stimulation (rTMS) at the left motor cortex (LMC) can significantly alleviate MTB related headache symptoms up to one month without significant side effects in comparison to sham control. Ongoing prospective clinical survey in patients receiving treatments also suggests rTMS provides a feasible non-invasive long-term therapeutic option for MTBI related headache (MTBI-HA) management. This proposal aims to further validate the long- term effect of rTMS in managing MTBI-HA up to 2-3 months by comparing the treatment effect of active-rTMS (Group A) to sham-rTMS (Group B) at LMC in: 1) reducing the intensity, frequency and duration of MTBI-HA and the overall analgesic usage; and 2) improving quality of life, mood and functions in patients with MTBI.