Functional electrical stimulation (FES) is one of the most common rehabilitation methods in purpose of recovery of paralyzed muscle by the means of sequential electrical stimulation. There are reports that in FES based therapy, like all rehabilitation, active participation of patient ensures better recovery result compared to simple stimulation itself. In this paper, we investigate the neurophysiological effect of participation intention of patient in rehabilitation therapy. To observe the difference in brain signal between intentional and involuntary movement during FES, electroencephalography (EEG) and near-infrared spectroscopy (NIRS) was simultaneously measured in motor cortex area. The result revealed the presence of intention affects activation of the brain significantly, and classification result showed higher than 80% accuracy performance. The result of this study implies the possibility for quantification in motivation for rehabilitation, which has not been considered as an absolute measurable value in rehabilitation area.