In recent years, efforts have focused on investigating the neurophysiological changes that occur in the brain after stroke, and on developing novel strategies such as additional brain stimulation to enhance sensorimotor and cognitive recovery. In the 1990s, repetitive transcranial magnetic stimulation (rTMS) was introduced as a therapeutic tool for improving the efficacy of rehabilitation for recovery after stroke. It is evident that disturbances of interhemispheric processes after stroke result in a pathological hyperactivity of the intact hemisphere. The rationale of using rTMS as a complementary therapy is mainly to decrease the cortical excitability in regions that are presumed to hinder optimal recovery by low-frequency rTMS delivered to the unaffected hemisphere, while high-frequency rTMS delivered to the affected hemisphere facilitates cortical excitability. However, the exact mechanisms of how rTMS works are still under investigation. There is a growing body of research in stroke patients investigating the effect of rTMS on facilitating recovery by modifying cortical and subcortical networks. Clinical trials applying rTMS already yielded promising results in improving recovery of sensorimotor and cognitive functions. Altogether, in combination with conventional therapeutic approaches, rTMS has a potential to become a complementary strategy to enhance stroke recovery by modulating the excitability of targeted brain areas. In future studies, emphasis should be placed on selecting patient populations to determine whether treatment response depends on age, lesion acuteness, or stroke severity. Furthermore, it is important to identify parameters optimizing the beneficial effects of rTMS on stroke recovery, and to monitor their long-term effects.