Motor imagery is suggested to stimulate the same plastic mechanisms in the brain as a real movement. The brain-computer interface (BCI) controls motor imagery by converting EEG during this process into the commands for an external device. This article presents the results of two-stage study of the clinical use of non-invasive BCI in the rehabilitation of patients with severe hemiparesis caused by focal brain damage. It was found that the ability to control BCI did not depend on the duration of a disease, brain lesion localization and the degree of neurological deficit. The first step of the study involved 36 patients; it showed that the efficacy of rehabilitation was higher in the group with the use of BCI (the score on the Action Research Arm Test (ARAT) improved from 1 [0; 2] to 5 [0; 16] points, p = 0.012; no significant improvement was observed in control group). The second step of the study involved 19 patients; the complex BCI-exoskeleton (i.e. with the kinesthetic feedback) was used for motor imagery trainings. The improvement of the motor function of hands was proved by ARAT (the score improved from 2 [0; 37] to 4 [1; 45:5] points, p = 0.005) and Fugl-Meyer scale (from 72 [63; 110 ] to 79 [68; 115] points, p = 0.005).