Despite the widespread use of repetitive transcranial magnetic stimulation (rTMS) in both research and clinical settings, there is a paucity of evidence regarding the effects of its application on neural activity. Studies investigating the effects of rTMS on human participants (Huang et al., 2005) have shown that patterned trains of rTMS can be used to modulate the sensitivity of motor pathways for a period outlasting the stimulation itself. These changes are often attributed to an rTMS-induced increase in neural "plasticity" or a "change in excitability" of the motor pathway. Evidence that rTMS can modify the strength of motor pathways has led to its introduction into stroke rehabilitation research. It is hypothesized that post-stroke, rTMS can enhance plasticity induction within the brain and, when combined with manual therapy, can facilitate surviving neurons assuming the function of those lost to the stroke (Hsu et al., 2012). In practice however, despite a multitude of studies investigating this approach, there remains no convincing evidence that rTMS is capable of promoting sustained long-term improvement in recovery, above the effects of rehabilitation alone (Hsu et al., 2012; Lefaucheur et al., 2014). We are of the opinion that a lack of advancement within the field is due to an incomplete understanding of the effects of TMS on neural elements. Here we discuss some of the existing evidence and propose experimental approaches that may enhance the human application of rTMS.