Previous functional magnetic resonance imaging (fMRI) studies reported inconsistent results for comparison in brain activation between migraine patients and healthy controls (HC). Thus, activation likelihood estimation (ALE) method, a powerful voxel-based technique, was used to explore the concordant functional brain changes in migraine patients.Studies published before October 2022 were searched in the following databases (PubMed, Web of Science and Google Scholar).Migraine without aura (MWoA) patients showed reduced amplitude of low-frequency fluctuations (ALFF) in right lingual gyrus, the left posterior cingulate and the right precuneus (PCUN), compared to HC. Migraine patients showed increased ALFF in the right claustrum, the left caudate, the left insula and the right parahippocampal gyrus, compared to HC. MWoA patients showed reduced regional homogeneity (ReHo) in the right culmen, compared to HC. In addition, migraine patients showed increased ReHo in the bilateral thalamus, compared to HC. MWoA patients showed reduced whole-brain functional connectivity (FC) in the left middle occipital gyrus and the right superior parietal lobule, compared to HC. In addition, migraine patients showed increased whole-brain FC in the left middle temporal gyrus (MTG), the right inferior frontal gyrus, the right superior temporal gyrus (STG) and the left inferior temporal gyrus, compared to HC.ALE analysis identified consistent functional changes in widespread regions, especially in cingulate gyrus, basal ganglia region and frontal cortex in migraine. These regions involve in pain processing, cognitive dysfunction and emotional problems. These results may provide important clues for clarifying the pathophysiology of migraine.