A robust, visual masking test that was developed to be feasible with functional magnetic resonance imaging (fMRI) was used to examine the visual cortical inhibitory function in migraine patients with visual aura at both psychophysical and cortical levels. The study showed that the decreased visibility of a visual target was associated with a reduction in cortical activation in the primary visual cortex. The suppression of the transient on-response and after-discharge of neurons to the target was most likely to be responsible for reducing cortical activation, rendering the target less visible or invisible. The migraine patients were equally susceptible to visual masking and showed no difference in cortical activation when compared with age- and sex-matched non-headache controls, demonstrating that visual cortical inhibitory function was not impaired under the experimental conditions. Although these results are not in conflict with the general cortical hyperexcitability theory in migraine, they provide evidence to show the limitation to the theory.