Repetitive transcranial magnetic stimulation (rTMS) can generate an increase or a decrease of neuronal excitability, which can modulate cognition and behaviour. Transcranial magnetic stimulation-induced cortical changes have been shown to result in neural plasticity. Thus, TMS provides an important opportunity to gain more insight into the mechanisms responsible for the remarkable flexibility of the central nervous system. The aim of this review was to cover the topics that could be useful when using TMS in the cognitive rehabilitation field after brain damage. The basic TMS principles are introduced, together with the clinical application for diagnosis and prognosis, the biological aspects, and the use in cognitive neuroscience studies. Finally, several hypotheses are discussed to explain the likely mechanisms induced by TMS that favour the recovery of a function after brain damage and cause the adult brain to undergo plasticity. The possibility of non-invasively interacting with the functioning of the brain and its plasticity mechanisms - a possibility that may eventually lead to cognitive and behavioural modifications - opens new and exciting scenarios in the cognitive neurorehabilitation field.