Objective: Non-invasive brain stimulation (NIBS) is beneficial to adult patients with depression, but its safety and efficacy in combination with antidepressants in children and adolescents with depression are not clear. We conducted a preliminary meta-analysis to objectively evaluate its clinical effect and provide information for future research and clinical practice. Methods: PubMed, Cochrane Library, Embase, and Web of Science were searched systematically to find clinical trials published in English before April 11, 2023. Stata software was used for meta-analysis, and random or fixed effect models were used to combine effect sizes. Results: Nine studies were eligible and included (n = 393). No articles about children were included in the analysis. The results showed that the remission rate was 40% (95% confidence interval [CI]: 13% to 71%). The scores of Children's Depression Rating Scale (CRDS) and Hamilton's depression scale (HAMD) significantly decreased compared to baseline value (MD = -27.04, 95% CI: -30.95, -23.12 and MD = -12.78, 95% CI: -19.55 to -6.01). In addition, the incidence of all adverse events was 13% (95% CI: 5%, 23%), and all were minor pain-related events. Conclusion: The combination of NIBS and antidepressants has been shown to notably alleviate depressive symptoms in adolescents, offering a considerable level of safety. This therapeutic synergy is particularly effective in patients with major depressive disorder, where repetitive transcranial magnetic stimulation augmented with antidepressants can enhance the amelioration of depressive symptoms. Systematic review registration: https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42023442215, PROSPERO CRD42023442215.