Background. Evidence suggests that brain-computer interface (BCI)-basedrehabilitation strategies show promise in overcoming the limited recovery potentialin the chronic phase of stroke. However, the specific mechanisms driving motorfunction improvements are not fully understood.Objective. We aimed at elucidating the potential functional brain connectivitychanges induced by BCI training in participants with chronic stroke.Methods. A longitudinal crossover design was employed with two groups ofparticipants over the span of 4 weeks to allow for within-subject (n = 21) and cross-group comparisons. Group 1 (n = 11) underwent a 6-day motor imagery-based BCItraining during the second week, whereas Group 2 (n = 10) received the sametraining during the third week. Before and after each week, both groups underwentresting state functional MRI scans (4 for Group 1 and 5 for Group 2) to establish abaseline and monitor the effects of BCI training.Results. Following BCI training, an increased functional connectivity was observedbetween the medial prefrontal cortex of the default mode network (DMN) and motor-related areas, including the premotor cortex, superior parietal cortex, SMA, andprecuneus. Moreover, these changes were correlated with the increased motorfunction as confirmed with upper-extremity Fugl-Meyer assessment scores,measured before and after the training.Conclusions. Our findings suggest that BCI training can enhance brain connectivity,underlying the observed improvements in motor function. They provide a basis fordeveloping novel rehabilitation approaches using non-invasive brain stimulation fortargeting functionally relevant brain regions, thereby augmenting BCI-inducedneuroplasticity and enhancing motor recovery.