Functional electrical stimulation (FES) is a standard rehabilitation approach applied by therapists to aid motor recovery in a paretic limb post-stroke. Information pertaining to the timing of a movement attempt can be obtained from changes in the power of oscillatory electrophysiological activity in motor cortical regions, derived from scalp electroencephalographic (EEG) recordings. The use of a brain–computer interface (BCI), to enable delivery of FES within a tight temporal window with a movement attempt detected in scalp EEG, is associated with greater motor recovery than conventional FES application in patients in the chronic phase post-stroke. We hypothesized that the heightened neural plasticity early post-stroke could further enhance motor recovery and that motor improvements would be accompanied by changes in the motor cortical sensorimotor rhythm after compared with before treatment. Here we assessed clinical outcome and changes in the sensorimotor rhythm in patients following subcortical stroke affecting the non-dominant hemisphere from a study comparing timing of FES delivery using a BCI, with a Sham group, receiving FES with no such temporal relationship. The BCI group showed greater clinical improvement following the treatment, particularly early post-stroke, and a greater decrease in beta oscillatory power and long-range temporal correlation over contralateral (ipsilesional) motor cortex. The electrophysiological changes are consistent with a reduction in compensatory processes and a transition towards a subcritical state when movement is triggered at the time of movement detection based on motor cortical oscillations.