Visual aura is present in about one-third of migraine patients and triggering by bright or flickering lights is frequently reported. Using migraine with visual aura patients, we investigated the neurochemical profile of the visual cortex using magnetic resonance spectroscopy. Specifically, glutamate/creatine and GABA/creatine ratios were quantified in the occipital cortex of female migraine patients. GABA levels in the occipital cortex of migraine patients were lower than that of controls. Glutamate levels in migraine patients, but not controls, correlated with the blood-oxygenation-level-dependent (BOLD) signal in the primary visual cortex during visual stimulation. Migraine with visual aura appears to disrupt the excitation-inhibition coupling in the occipital cortex.