Abstract Neurofeedback training using electroencephalogram (EEG)-based brain–computer interfaces (BCIs) combined with mental rehearsals of motor behavior has demonstrated successful self-regulation of motor cortical excitability. However, it remains unclear whether the acquisition of skills to voluntarily control neural excitability is accompanied by structural plasticity boosted by neurofeedback. Here, we sought short-term changes in cortical structures induced by 30 min of BCI-based neurofeedback training, which aimed at the regulation of sensorimotor rhythm (SMR) in scalp EEG. When participants performed kinesthetic motor imagery of right finger movement with online feedback of either event-related desynchronisation (ERD) of SMR magnitude from the contralateral sensorimotor cortex (SM1) or those from other participants (i.e. placebo), the learning rate of SMR-ERD control was significantly different. Although overlapped structural changes in gray matter volumes were found in both groups, significant differences revealed by group-by-group comparison were spatially different; whereas the veritable neurofeedback group exhibited sensorimotor area-specific changes, the placebo exhibited spatially distributed changes. The white matter change indicated a significant decrease in the corpus callosum in the verum group. Furthermore, the learning rate of SMR regulation was correlated with the volume changes in the ipsilateral SM1, suggesting the involvement of interhemispheric motor control circuitries in BCI control tasks.