Recent studies support an association between substance use disorders (SUDs) and cortical excitability. Transcranial magnetic stimulation (TMS) is a non-invasive tool that can be used to assess cortical physiological processes (e.g., inhibition, excitation) and has proven to be a useful diagnostic tool in brain disorders associated with alterations in cortical excitability. In this manuscript, we review studies that employ TMS to evaluate cortical excitability in patients with SUDs. Furthermore, we discuss preliminary studies that examine repetitive TMS (rTMS) as a potential treatment for patients with SUDs. Although the use of TMS to evaluate and to treat those individuals with SUDs is in its early stages, these studies reveal significant alterations in both cortical inhibition and excitation. Specifically, elevated cortical inhibition was reported in both cocaine and nicotine dependent individuals, while one study demonstrated an increase in cortical excitability in those who use 3, 4-methylenedioxymethamphetamine (MDMA). Furthermore, three studies examining rTMS as a potential treatment in cocaine and nicotine addiction report decreases in the level of cravings and in the number of cigarettes smoked following rTMS administration to the dorsal lateral prefrontal cortex. Thus, TMS has provided early interesting findings vis a vis cortical excitability in SUDs. Moreover, preliminary evidence suggests that rTMS is efficacious in the treatment of cocaine and nicotine addiction. Further work is needed to enhance our understanding of the altered neurophysiology in SUDs as well as the ways in which rTMS treatment can be directed to optimize treatment.