Background: This study was conducted to evaluate the short-term therapeutic effects of using repeated transcranial magnetic stimulation (rTMS) to treat obsessive-compulsive disorder (OCD) and to examine potential influencing factors. Method: We searched the PubMed, EMBASE, CENTRAL, Wanfang, CNKI, and Sinomed databases on September 18, 2016 and reviewed the references of previous meta-analyses. Sham-controlled, randomized clinical trials using rTMS to treat OCD were included. Hedge's g was calculated for the effect size. Subgroup analyses and univariate meta-regressions were conducted. Results: Twenty studies with 791 patients were included. A large effect size (g=0.71; 95%CI, 0.55-0.87; P < 0.001) was found for the therapeutic effect. Targeting the supplementary motor area (SMA) (g=0.56; 95%CI, 0.12-1.01; P < 0.001), left dorsolateral prefrontal cortex (DLPFC) (g=0.47; 95%CI, 0.02-0.93; P=0.02), bilateral DLPFC (g=0.65; 95%CI, 0.38-0.92; P < 0.001) and right DLPFC (g=0.93; 95%CI, 0.70-1.15; P < 0.001), excluding the orbitofrontal cortex (OFC) (g=0.56; 95%CI, -0.05-1.18; P=0.07), showed significant improvements over sham treatments. Both low-frequency (g=0.73; 95%CI, 0.50-0.96; P < 0.001) and high frequency (g=0.70; 95%CI, 0.51-0.89; P < 0.001) treatments were significantly better than sham treatments, with no significant differences between the effects of the two frequencies. The subgroup analyses indicated that patients who were non-treatment resistant, lacked concurrent major depressive disorder (MDD) and received threshold-intensity rTMS showed larger therapeutic effects than the corresponding subgroups. The subgroup analysis according to sham strategy showed that tilted coils yielded larger effects than sham coils. Meta regression analyses revealed that none of the continuous variables were significantly associated with the therapeutic effects. Limitations: Only short-term therapeutic effects were assessed in this study. Conclusions: Based on this study, the short-term therapeutic effects of rTMS are superior to those of sham treatments. The site of stimulation, stimulation frequency and intensity and sham condition were identified as potential factors modulating short-term therapeutic effects. The findings of this study may inspire future research.