Background: Despite the considerable success of comprehensive tobacco control efforts, tobacco use remains one of the greatest preventable causes of death and disease today. Over half of all smokers in the US make quit attempts every year, but over 90% relapse within 12 months, choosing the immediate reinforcement of smoking over the long-term benefits of quitting. Conceptual and empirical evidence supports continued investigation of high frequency repetitive transcranial magnetic stimulation (rTMS) of the left dorsolateral prefrontal cortex in reducing relapse and decreasing cigarette consumption. While this evidence is compelling, an optimal dosing strategy must be determined before a long-term efficacy trial can be conducted. The goal of this study is to determine a dosing strategy for 20 Hz rTMS that will produce the best long-term abstinence outcomes with the fewest undesirable effects. Methods: This is a fully crossed, double-blinded, sham-controlled, 3x2x2 randomized factorial study. The three factors are duration (stimulation days: 8, 12, and 16); intensity (900 or 1800 pulses per day); and sham control. Participants (n = 258) will consist of adults (18-65) who are motivated to quit smoking cigarettes and who will be followed for 6 months post-quit. Outcomes include latency to relapse, point prevalence abstinence rates, delay discounting rates, cognitive-behavioral skills acquisition, and multiple measures of potential undesirable effects that impact participant compliance. Discussion: This study integrates existing theoretical concepts and methodologies from neuropsychology, behavioral economics, brain stimulation, clinical psychology, and the evidence-based treatment of tobacco dependence in the development of a promising and innovative approach to treat tobacco dependence. This study will establish an optimal dosing regimen for efficacy testing. Findings are expected to have a significant influence on advancing this approach as well as informing future research on clinical approaches that combine rTMS with other evidence-based treatments for tobacco dependence and perhaps other addictions.