Reactive response inhibition cancels impending actions to enable adaptive behavior in ever-changing environments and has wide neuropsychiatric implications. A canonical paradigm to measure the covert inhibition latency is the stop-signal task (SST). To probe the cortico-subcortical network underlying motor inhibition, transcranial magnetic stimulation (TMS) has been applied over central nodes to modulate SST performance, especially to the right inferior frontal cortex and the presupplementary motor area. Since the vast parameter spaces of SST and TMS enabled diverse implementations, the insights delivered by emerging TMS-SST studies remain inconclusive. Therefore, a systematic review was conducted to account for variability and synthesize converging evidence. Results indicate certain protocol specificity through the consistent perturbations induced by online TMS, whereas offline protocols show paradoxical effects on different target regions besides numerous null effects. Ancillary neuroimaging findings have verified and dissociated the underpinning network dynamics. Sources of heterogeneity in designs and risk of bias are highlighted. Finally, we outline best-practice recommendations to bridge methodological gaps and subserve the validity as well as replicability of future work.