Background: The purpose of this study was to use functional magnetic resonance imaging (fMRI) to quantify changes in brain activity during experimental occlusal interference. Methods: Fourteen healthy volunteers performed a rhythmical tapping occlusion task with experimental occlusal interference of the right molar tooth at 0 mm (no occlusion), 0.5 mm, and 0.75 mm. The blood-oxygen-level dependent (BOLD) signal was quantified using statistical parametric mapping and compared between rest periods and task periods. Results: In tapping tasks with experimental occlusal interference of 0.75 mm or 0.5 mm, there was clear activation of the contralateral teeth-related primary sensory cortex and Brodmann's area 46. At 0 and 30 minutes after removal of the experimental occlusal interference, the activation clearly appeared in the bilateral teeth-related primary sensory cortices and Brodmann's area 46. At 60 minutes after the removal of the experimental occlusal interference, the activation of Brodmann's area 46 had disappeared, and only the bilateral teeth-related primary sensory cortices were active. Conclusions: The present results suggest that adjustments for experimental occlusal interference can be objectively evaluated using fMRI. We expect that this method of evaluating adjustments in occlusal interference, combined with fMRI and the tapping task, could be applied clinically in the future.