Non-invasive brain stimulation (NIBS) is an emerging treatment for mental disorders that is painlessness and easy to administer. However, its effectiveness for treating fear extinction requires further elucidation. We searched eight bibliographical databases and identified randomized controlled trials of NIBS interventions for fear extinction in healthy populations. Outcomes were evaluated based on skin conductance response (SCR) under three experimental conditions: threat condition stimulation (CS+), safe condition stimulation (CS−), and their discrimination (CS+ minus CS−). We applied a random-effects model to determine effect sizes (Hedge’s g) post-intervention and assessed article quality using Physiotherapy evidence database (PEDro) scale. Twenty-one studies meeting systematic review criteria were included in this analysis, incorporating 40 independent effect sizes and data from 11 studies (n = 632) in the meta-analysis. Compared with the control group, the intervention group exhibited significant reductions SCRs: CS+ (g = −0.32, 95% confidence interval (CI) [−0.56, −0.07]) and discrimination (g = −0.35; 95% CI [−0.55, −0.15]). Fear extinction was more effective in the 24-hour test than immediately after NIBS. In conclusion, NIBS enhanced fear extinction, and the time interval between stimulus and testing may serve as a moderating variable.