The mechanisms underlying the locomotion recovery in poststroke patients remain unknown. Navigated transcranial magnetic stimulation (nTMS) is a new method to evaluate the functional state of the motor system. Using of the exoskeleton complex (EC) allow to correct walking pattern significantly. The aim of this study was to evaluate the capability of nTMS to assess changes in gait cortical control using EC in poststroke patients. 14 patients suffered subcortical stroke, mean age was 53.0 years [49, 62], mean duration of a stroke of 14.2 [7.0; 23.0] months were included. All patients trained with EC for 10 times and also received standardized physical therapy. All patients underwent nTMS, as well as clinical assessment using a Fugl-Meyer Scale lower extremity section and 10 m walking test before and after trains. A significant decrease of time to walk 10 meter was observed, while Fugl-Meyer Score remained unchanged. Patients showed the significant reduction of the average latency of motor responses from the affected hemisphere and different patterns of size and localization changes in both legs' cortical motor areas. Navigates TMS may demonstrate individual patterns of changes in cortical representation of leg muscles in post-stroke patients with damage of various motor system elements, while using exoskeleton complex. Thus, navigated TMS may be used not only for verification of neuroplasticity process, but it may also provide its detailed description.