BACKGROUND: Cardiovascular autonomic system (ANS) may be affected by altered neural activations in the brain. This systematic review and meta-analysis investigated potential effects of repetitive transcranial magnetic stimulation (rTMS) protocols on cardiovascular ANS control. METHODS: Through 19 qualified studies, we acquired 70 comparisons for data synthesis. Individual effect sizes were estimated by comparing changes in following cardiovascular ANS control variables between active and sham stimulation conditions: (a) blood pressure (BP), (b) heart rate (HR), and (c) heart rate variability (HRV). Moreover, two moderator variable analyses determined whether changes in cardiovascular ANS control were different based on (a) rTMS protocols (excitatory rTMS versus inhibitory rTMS) and (b) specific targeted cortical regions, respectively. RESULTS: The random-effects model meta-analysis revealed significant improvements in cardiovascular ANS control after the rTMS protocols. Specifically, applying excitatory and inhibitory rTMS protocols significantly decreased values of BP and HR variables. For HRV variables, excitatory rTMS protocols showed significant positive effects. These improvements in cardiovascular ANS control were observed while applying either excitatory rTMS protocols to the left dorsolateral prefrontal cortex or inhibitory rTMS protocols to the right dorsolateral prefrontal cortex. LIMITATIONS: Relatively small number of studies for inhibitory rTMS on the right dorsolateral prefrontal cortex were included in this meta-analysis. CONCLUSION: These findings suggest that applying excitatory and inhibitory rTMS protocols on prefrontal cortical regions may be effective to improve cardiovascular ANS control.