The aim of this systematic review and meta-analysis was to evaluate the efficacy of noninvasive brain stimulation (NIBS) on cognition using functional magnetic resonance imaging (fMRI) in patients with mild cognitive impairment (MCI) and Alzheimer's disease (AD), thus providing the neuroimaging mechanism of cognitive intervention.English articles published up to April 30, 2023 were searched in the PubMed, Web of Science, Embase, and Cochrane Library databases. We included randomized controlled trials where resting-state fMRI was used to observe the effect of NIBS in patients with MCI or AD. RevMan software was used to analyze the continuous variables, and SDM-PSI software was used to perform an fMRI data analysis.A total of 17 studies comprising 258 patients in the treatment group and 256 in the control group were included. After NIBS, MCI patients in the treatment group showed hyperactivation in the right precuneus and decreased activity in the left cuneus and right supplementary motor area. In contrast, patients in the control group showed decreased activity in the right middle frontal gyrus and no hyperactivation. The clinical cognitive scores in MCI patients were significantly improved by NIBS, while not in AD. Some evidence regarding the modulation of NIBS in resting-state brain activity and functional brain networks in patients with AD was found.NIBS could improve cognitive function in patients with MCI and AD. fMRI evaluations could be added to evaluate the contribution of specific NIBS treatment therapeutic effectiveness.© 2023 The Authors. CNS Neuroscience & Therapeutics published by John Wiley & Sons Ltd.