While it is well-known that neuronal activity promotes plasticity and connectivity, the success of activity-based neural rehabilitation programs remains extremely limited in human clinical experience because they cannot adequately control neuronal excitability and activity within the injured brain in order to induce repair. However, it is possible to non-invasively modulate brain plasticity using brain stimulation techniques such as repetitive transcranial (rTMS) and transcranial direct current stimulation (tDCS) techniques, which show promise for repairing injured neural circuits (Henrich-Noack et al., 2013; Lefaucher et al., 2014). Yet we are far from having full control of these techniques to repair the brain following neurotrauma and need more fundamental research (Ellaway et al., 2014; Lefaucher et al., 2014). In this perspective we discuss the mechanisms by which rTMS may facilitate neurorehabilitation and propose experimental techniques with which magnetic stimulation may be investigated in order to optimise its treatment potential.