Motor imagery training under the control of a brain-computer interface (BCI) facilitates motor recovery after stroke. The efficacy of BCI based on electroencephalography (EEG-BCI) has been confirmed by several meta-analyses, but a more convenient and noise-resistant method of near-infrared spectroscopy in the BCI circuit (NIRS-BCI) has been practically unexamined; comparisons of the two types of BCI have not been performed.Objective: to compare the control accuracy and clinical efficacy of NIRS-BCI and EEG-IMC in post-stroke rehabilitation.Material and methods. The NIRS-BCI group consisted of patients from an uncontrolled study (n=15; 9 men and 6 women; age – 59.0 [49.0; 70.0] years; stroke duration – 7.0 [2.0; 10.0] months; upper limb paresis – 47.0 [35.0; 54.0] points on the Fugl-Meyer Assessment for motor function evaluation of the upper limb – FM-UL). The EEG-IMC group was formed from the main group of the randomized controlled trial “iMove” (n=17; 13 men and 4 women; age – 53.0 [49.0; 70.0] years; stroke duration – 10.0 [6.0; 13.0] months; upper limb paresis – 33.0 [12.0; 53.0] points on the FM-UL). Patients participated in a comprehensive rehabilitation program supplemented by BCI-guided movement imagery training (average of 9 training sessions).Results. Median of average BCI control rates achieved by the patients was 46.4 [44.2; 60.4]% in the NIRS group and 40.0 [35.7; 45.1]% in the EEG group (p=0.004). For the NIRS-BCI group, the median of the maximum BCI control accuracy achieved was 66.2 [56.4; 73.7]%, for EEGBCI – 50.6 [43.0; 62.3]% (p=0.006). The proportion of patients who achieved a clinically significant improvement according ARAT and the proportion of patients who achieved a clinically significant improvement according FM-UL were comparable in both groups. The NIRS-BCI group showed greater improvement in motor function compared to the EEG-BCI group according to Action Research Arm Test (ARAT; an increase of 5.0 [4.0; 8.0] points compared to an increase of 1.0 [0.0; 3.0] points; p=0.008), but not according to FM-UL scale (an increase of 5.0 [1.0; 10.0] and 4.0 [2.0; 5.0] points, respectively; p=0.455).Conclusion. NIRS-BCI has an advantage in control accuracy and ease of use in clinical practice. Achieving higher control accuracy of BCI provides additional opportunities for the use of game feedback scenarios to increase patient motivation.