Objective To evaluate the effectiveness of repetitive transcranial magnetic stimulation (rTMS) in treating stroke patients with motor dysfunction. Methods The Cochrane Library, MEDLINE, EMbase, CBM, CNKI and WanFang Data were searched from inception to January 2012, and the references of the included studies were also retrieved to collect the randomized controlled trials (RCTs) on rTMS in treating stroke patients with motor dysfunction. Two reviewers independently screened articles according to the inclusion and exclusion criteria, extracted data and evaluated the quality of the included studies. Then meta-analysis was performed using RevMan 5.0.2 software, and evidence quality and recommendation level were assessed using the GRADE system. Results A total of 11 RCTs involving 376 patients were included. The results of meta-analysis (including 3 RCTs, low quality) showed that, compared with the routine rehabilitation treatment, 2 to 4 weeks of rTMS was much beneficial to stroke patients with motor dysfunction, with significant differences (WMD=11.02, 95%CI 2.56 to 19.47). The other 8 studies only adopted descriptive analysis accordingly. Conclusion It is still uncertain of the effectiveness of rTMS in improving motor dysfunction of stroke patients, so rTMS should be applied with caution in clinic.