This study aims to quantitatively evaluate and summarize the effectiveness of repetitive transcranial magnetic stimulation (rTMS) in the treatment of patients with multiple sclerosis (MS). Methods: The PubMed, EMBASE, Web of Science, Cochrane Database of Systematic Reviews, CBM, CNKI and Wanfang databases were searched for randomized controlled trails (RCTs) from their inception through July 10, 2021. RCTs that met the inclusion and exclusion criteria were included in the study, and RevMan software was used for meta-analysis. Outcome indicators included scores on the fatigue severity scale (FSS), modified Ashworth scale (MAS) and the H/M amplitude ratio of the Soleus H reflex. When p < 0.05, the difference was considered significant. Results: A total of 10 articles were included in this study, with 8 of them in the quantitative synthesis. The metaanalysis showed that the short-term effect of rTMS treatment for the MAS was better than that of the control treatment (95% CI: − 1.27 to − 0.25, p = 0.004); and compared with the control group, the effect of rTMS treatment for the H/M ratio showed a significant effect (95% CI: − 0.12 to − 0.03, p = 0.002); while the treatment effect for the FSS was not significant (95% CI: − 4.87 to 1.28, p = 0.25). Conclusion: Our results provide preliminary evidence for the treatment of patients with MS by rTMS, especially for improving spasticity, but further research is needed to evaluate its effects on fatigue.