BACKGROUND: The main symptoms of myelopathy associated with human T-cell lymphotropic virus type 1 or tropical spastic paraparesis (HAM / TSP) are the presence of high intensity pain in the lower back, spasticity and weakness in the lower limbs, loss of balance and difficulties in locomotion. Pulsed Transcranial Magnetic Stimulation (rTMS) has been able to influence cortical plasticity, decreasing spasticity, increasing motor performance and promoting analgesia in several similar conditions. OBJECTIVE: To analyze the effect of neuromodulation by pulsed transcranial magnetic stimulation (rTMS) on pain and functional mobility in individuals with HAM / TSP. METHODOLOGY: A randomized clinical trial will be conducted in a sample made up of 40 participants randomly allocated into two groups: Sham Group (SG) with 20 and Test Group (TG) with 20 patients. Individuals aged> 20 years, community walkers with or without orthosis, with chronic pain (? 6 months) in the lumbar region and / or lower limbs will be included. Individuals with epilepsy, cancer, pregnant women, patients with cardiac pacemakers, metallic implants in the brain or skull, users of illicit drugs and / or use of controlled medications in the last six months will be excluded. The protocol will be applied for 10 consecutive days with eight months of follow-up. Our hypothesis is that when using rTMs according to the proposed procedure, it will be possible to relieve pain and improve the functional mobility of these individuals with a long-lasting effect. CONCLUSION: We hope that rTMS is a promising treatment to reduce pain intensity and to improve functional mobility in individuals undergoing active modality. We declare this protocol a promising resource for the treatment of htlv-1 individuals in reducing pain and improving functional mobility. Yes, this protocol has already been applied to 6 patients. However, with the pandemic the study had to be discontinued. However, despite the small sample size and not being fully applied as suggested by the protocol, it was possible to notice a satisfactory result of the intervention. Thus, the application of this protocol can contribute to identify the result of this therapeutic modality in a safer way, as well as assist in the treatment of symptoms of this population, favoring a better quality of life.