Transcranial magnetic stimulation (TMS) is a non-invasive method for targeted modulation of the electrical activity of brain neurons with a magnetic field. Although TMS efficacy was demonstrated in the treatment of several neurological and mental disorders, changes in nervous tissue at the cellular and molecular levels with different duration and intensity of stimulation have been relatively understudied by cellular neurobiology methods. Aim. The aim of this review was to evaluate and summarize new experimental data on the fundamental mechanisms underlying the action of TMS and its potential in modulating structural and functional changes in nervous tissue. This article summarizes recent data on the effects of different TMS protocols on the mechanisms underlying synaptic plasticity, neurogenesis, and neuronal differentiation. Separate sections summarize the neuroprotective effects of this method and glial microenvironment response. Studies to investigate the mechanisms of TMS will contribute to the development of more effective and reliable treatment protocols.