As stereoscopic displays have spread, it is important to know what really causes the visual fatigue and discomfort and what happens in the visual system in the brain behind the retina while viewing stereoscopic 3D images on the displays. In this study, functional magnetic resonance imaging (fMRI) was used for the objective measurement to assess the human brain regions involved in the processing of the stereoscopic stimuli with excessive disparities. Based on the subjective measurement results, we selected two subsets of comfort videos and discomfort videos in our dataset. Then, a fMRI experiment was conducted with the subsets of comfort and discomfort videos in order to identify which brain regions activated while viewing the discomfort videos in a stereoscopic display. We found that, when viewing a stereoscopic display, the right middle frontal gyrus, the right inferior frontal gyrus, the right intraparietal lobule, the right middle temporal gyrus, and the bilateral cuneus were significantly activated during the processing of excessive disparities, compared to those of small disparities (< 1 degree).