Neural plasticity is defined as a reshape of communication paths among neurons, expressed through changes in the number and weights of synaptic contacts. During this process, which occurs massively during early brain development but continues also in adulthood, specific brain functions are modified by activity-dependent processes, triggered by external as well as internal stimuli. Since transcranial magnetic stimulation (TMS) produces a non-invasive form of brain cells activation, many different TMS protocols have been developed to treat neurological and psychiatric conditions and proved to be beneficial. Although neural plasticity induction by TMS has been widely assessed on human subjects, we still lack compelling evidence about the actual biological and molecular mechanisms. To support a better comprehension of the involved phenomena, the main focus of this review is to summarize what has been found through the application of TMS to animal models. The hope is that such integrated view will shed light on why and how TMS so effectively works on human subjects, thus supporting a more efficient development of new protocols in the future.