Using functional magnetic resonance imaging (fMRI) and near-infrared spectroscopy (NIRS), we examined the role of periodontal afferent inputs on cerebral activation pattern evoked by masticatory muscle activity in twenty-two subjects. Statistical comparisons were used to identify brain regions with significant activation after subtraction of baseline activity from sham teeth-tapping (no periodontal input) and teeth-tapping (periodontal input) activity in an fMRI (N = 14) and NIRS study (N = 8). Both sham teeth-tapping and teeth-tapping significantly activated bilateral sensorimotor cortex and supplementary motor area in the fMRI study. NIRS revealed that oxygenated hemoglobin concentrations increased in sensorimotor cortex; however, there was no significant difference in degree of oxygenated hemoglobin changes between sham teeth-tapping and teeth-tapping. A control study (N = 8) characterized the jaw muscle activity and amplitude of the two motor tasks and demonstrated significantly higher electromyogram (EMG) activity in the jaw closing muscles during teeth contact in the teeth-tapping session. Since the cerebral activation during sham teeth-tapping and teeth-tapping was similar, we suggest that the influence of periodontal afferent inputs and associated jaw muscle activity is relatively minor compared to the rhythmic jaw movements. Although the clinical significance of the present findings remains unknown, they may have implications for the understanding of awake or sleep-related bruxism characterized by subconscious and rhythmic teeth-grinding or teeth-clenching.