In this article, the results of the authors’ research, including analysis of the clinical and instrumental data concerning 203 patients with, stroke are presented. It is shown that the clinical effectiveness of the transcranial methods incorporated in the combined rehabilitation programs depends on the type of stroke and localization of the lesions. Specifically, the patients presenting with ischemic stroke of hemispheric localization experienced a neurophysiologically confirmed significant clinical improvement that became apparent after the consistent application of transcranial magnetic therapy and micropolarization. In the patients with ischemic stroke of stem localization, the positive influence on psychomotor recovery was achieved with the application of transcranial magnetic therapy, but transcranial micropolarization did not have an appreciable effect on the recovery of such patients. The patients presenting with hemorrhagic stroke did not experience any significant improvement of psychomotor parameters from transcranial magnetic therapy and transcranial micropolarization. The likely mechanism underlying the recovery of psychomotor processes under effect of transcranial magnetic therapy in the patients with ischemic stroke is the normalization of the frequency of interaction between brain structures. In addition, in the patients with ischemic stroke of hemispheric localization and in the patients with hemorrhagic stroke electrical myostimulation has a marked impact on the psychomotor recovery only in case of functional treatment. In the patients suffering from ischemic stroke of stem localization non-functional electromyostimulation significantly improves motor functions and cognitive motor control.