fMRS has been used in migraine and pain research. It has supported the important hypothesis of mitochondria dysfunction in migraine with aura (MwA) patients. Here the ability of fMRS to measure chemical processes in the brain over time proved crucial for confirming that repetitive photic stimulation causes higher increase of the lactate level and higher decrease of the  N-acetylaspartate (NAA) level in the visual cortex of MwA patients compared to migraine without aura (MwoA) patients and healthy individuals.
In pain research fMRS complements fMRI and PET techniques. Although fMRI and PET are continuously used to localize pain processing areas in the brain, they can not provide direct information about changes in metabolites during pain processing that could help to understand physiological processes behind pain perception and potentially lead to novel treatments for pain. fMRS overcomes this limitation and has been used to study pain-induced (cold-pressure, heat, dental pain) neurotransmitter level changes in the anterior cingulate cortex, anterior insular cortex and left insular cortex. These fMRS studies are valuable because they show that some or all Glx compounds (glutamate, GABA and glutamine) increase during painful stimuli in the studied brain regions.