Electroencephalogram-based brain-computer interfaces (BCI) have been used as a potential tool for training volitional regulation of corticomuscular drive in patients who have severe hemiplegia due to stroke. However, it is unclear whether ERD observed while attempting motor execution can be regarded as a neural marker that represents M1 excitability in survivors of severe stroke. Therefore we investigated the association between ERD and the blood-oxygen-level-dependent (BOLD) fMRI signal during attempted movement of a paralyzed finger in stroke patients. Nine chronic stroke patients received BCI training for finger extension movement 1 h daily for a duration of 1 month. The sensorimotor rhythm was recorded from the sensorimotor area of the damaged hemisphere, and ongoing amplitude variations were monitored using a BCI system. Either a visual alert or the action of a motor-driven orthosis was triggered in response to ERD of the sensorimotor rhythm while patients attempted extension movements of the paralyzed fingers. Inter-subject covariance between ERD and the BOLD response in the sensorimotor areas was calculated. After BCI training, an increased ERD over the damaged hemisphere was confirmed in all participants while they attempted extension of the affected finger and this increase was associated with a BOLD response in primary sensorimotor area. Whole-brain MRI revealed that the primary sensorimotor area and supplementary motor area were activated in the damaged hemisphere after 1 month of BCI training. ERD reflects the BOLD responses of the primary motor areas in either hemisphere while patients who have severe chronic hemiplegia due to a stroke attempt an extension movement of the paralyzed fingers. One month of BCI can alter motor-related brain area activation. Combining BCI with other methods to facilitate such changes may help to implement BCI for motor rehabilitation after stroke.