In this study, we tried to identify the cortical areas associated with the experience of visual discomfort in the viewing of stereoscopic images. To this purpose, we first conducted a subjective assessment experiment to select, based on viewers' opinions, two sets of stereoscopic video sequences: one comprising video sequences generally rated as comfortable and the other comprising video sequences generally rated as uncomfortable. The two sets differed mainly with respect to the absence or presence of excessive screen disparities. Next, we used these video sequences as stimuli in two functional magnetic resonance imaging (fMRI) experiments so that we could identify differences, if any, in brain activation while viewing comfortable and uncomfortable video sequences. We found that, compared to comfortable videos with small screen disparities, uncomfortable videos with excessive screen disparities resulted in significantly higher levels of activation in the following brain areas: the right middle frontal gyrus (MFG), the right inferior frontal gyrus (IFG), the right inferior parietal lobule (IPL), the right middle temporal gyrus (MTG), the bilateral lingual gyri, the bilateral cuneus, and the right precuneus. The results of the fMRI experiments suggest that visual discomfort due to excessive screen disparities can be caused by sensory (related with the subjective sensation of fusion difficulty and vision clarity) and/or motor (related with unnatural eye movements) phenomena. The intraparietal sulcus (IPS) regions in the human brain may be involved in the sensory phenomenon, and the frontal eye field (FEF), premotor cortex, and IPS regions may be involved in the motor phenomenon.