Functional magnetic resonance imaging (fMRI) is an imaging method that enables us to understand brain anatomy, mapping and its function. While fMRI was previously used in experimental studies, it has now been used in clinical studies. Imaging in fMRI is based on measuring the increase in regional blood flow caused by cortical activation. fMRI indirectly demonstrates neural activation by detecting increases in oxygenation. fMRI relies on the sensitivity of magnetic resonance signals to changes in deoxyhemoglobin levels or perfusion, reflecting the metabolic and hemodynamic responses associated with neural activation. Imaging is arranged in the clinic for primary headaches if needed for a differential diagnosis. However, imaging studies are utilized in scientific research to elucidate the pathophysiology. Migraine is a common episodic disorder characterized by recurring attacks. Investigating the functional structure of the brain during both attack and interictal periods is crucial in understanding migraine pathology. However, capturing patients' migraine attacks for monitoring purposes without treatment is considered unethical in many countries. Moreover, conducting such studies is hindered by the requirement for prolonged hospital stays and extended imaging times, which significantly increase costs. Despite the challenges of conducting research in migraine patients, fMRI stands out as an excellent imaging method for investigating the functional brain structures involved in this episodic disorder. Several fMRI studies have yielded valuable insights into the pathophysiology of migraine. fMRI is believed to offer valuable guidance in refining our understanding of migraine-specific mechanisms, facilitating biomarker studies for migraine activity, and elucidating abnormal functions in regions affected by migraine. Monitoring treatment response using biomarkers is anticipated to be an effective tool for identifying targets for migraine treatment, including assessing treatment efficacy in the development of new migraine-specific therapies.