Functional electrical stimulation (FES) is a common rehabilitation method for the purpose of recovery of paralyzed muscle by means of sequential electrical stimulation. Reports indicate that active participation by the patient, as opposed to simple stimulation, leads to improved recovery when using FES and other rehabilitation techniques. In this paper, we investigate the neurophysiological effect of an active participant's intention in the FES rehabilitation task. To observe the difference in brain signal between intentional and involuntary movement during FES, electroencephalography and near-infrared spectroscopy were simultaneously measured in the motor cortex area. The result showed that the presence of intention affects the activation of the brain significantly in both hemodynamic responses (near-infrared spectroscopy) and electrical (electroencephalography) patterns, and the accuracy of classification between passive and active mental states during FES was 85.3%. Our result implies the possibility to quantify motivation, or active participation, during rehabilitation, which has not been considered a measurable value in the rehabilitation field.