Advance medical technologies improved the survival of patients after brain injury. As a result of this, the number of disorder of consciousness cases is on the rise. Exogenous depolarization of neuronal ensembles and associative connections between neurons that potentially have a neuromodulation effect can increase the level of consciousness. Transcranial magnetic stimulation (TMS) is applied to neurodegenerative diseases, pain syndromes, depressive disorders, and various degree of disorder of consciousness. The use of TMS in post-anoxic injury has the most pessimistic outcome, whereas more promising results come in the traumatic brain injury. This difference is because of the difference in the localization of injury that is a key factor in determining the difference in the therapeutic response in patients after TMS. Several factors play a vital role in the use method of TMS, the combination or personalization of therapeutic protocols, and the feasibility of this method in various pathological conditions.