The theory of "visual stress" holds that visual discomfort results from overactivation of the visual cortex. Despite general acceptance, there is a paucity of empirical data that confirm this relationship, particularly for discomfort from visual flicker. We examined the association between neural response and visual discomfort using flickering light of different temporal frequencies that separately targeted the magnocellular, parvocellular, and koniocellular post-receptoral pathways. Given prior work that has shown larger cortical responses to flickering light in people with migraine, we examined 10 headache free people and 10 migraineurs with visual aura. The stimulus was a uniform field, 50 degrees in diameter, that modulated with high-contrast flicker between 1.625 and 30 Hz. We asked subjects to rate their visual discomfort while we recorded steady state visually evoked potentials (ssVEP) from primary visual cortex. The peak temporal sensitivity ssVEP amplitude varied by post-receptoral pathway, and was consistent with the known properties of these visual channels. Notably, there was a direct, linear relationship between the amplitude of neural response to a stimulus and the degree of visual discomfort it evoked. No substantive differences between the migraine and control groups was found. These data link increased visual cortical activation with the experience of visual discomfort.