Objective To systematically evaluate the efficacy of repetitive transcranial magnetic stimulation (rTMS) in reducing comorbid anxiety and depressive symptoms in patients with obsessive-compulsive disorder (OCD). Methods Three electronic databases were searched for randomized, sham-controlled clinical trials evaluating rTMS for the treatment of OCD. Hedge's g was calculated as the effect size for anxiety/depression symptom severity (primary outcome) and OCD severity (secondary outcome). Subgroup analyses and meta-regression analyses were carried out to evaluate the most promising target and whether a reduction in OCD severity moderates the change in anxiety or depression scores. Results Twenty studies ( n = 688) were included in the meta-analysis. rTMS had small-medium effect size on OCD (Hedge's g = 0.43; 95% confidence interval [CI]: [0.20, 0.65]; P < 0.001), anxiety (Hedge's g = 0.3; 95% CI: [0.11, 0.48]; P = 0.001) and depression (Hedge's g = 0.24; 95% CI: [0.07, 0.40]; P = 0.003) symptoms. Subgroup analysis showed that protocols targeting dorsolateral prefrontal cortex (DLPFC) were effective for 3 outcome measures. The change in anxiety, but not depression severity, was moderated by a change in OCD symptom scores. However, the findings are uncertain as a majority of the studies had some concerns or a high risk of bias. Conclusions Active rTMS protocol targeting DLPFC is effective in reducing the comorbid anxiety/depression symptoms along with OCD severity. The antidepressant effect is not moderated by the anti-obsessive effect of rTMS.