Repetitive transcranial magnetic stimulation (rTMS) is a non-invasive neurophysiological technique. Pre-clinical and clinical studies supported that rTMS might have antidepressant effects. However, whether antidepressant effect of chronic rTMS is gender-dependent is still unknown. In this study, male and female Wistar rats received 10-day rTMS (4 trains of 15 Hz; 200 stimuli/day; 1.0 T) or control condition, and then were subjected to the forced-swim test (FST). We found that female rats consistently showed higher activity levels than males in FST and revealed the significant effects of gender and rTMS as well as the interaction of gender and rTMS. The result suggested the antidepressant-like effects of chronic rTMS on behavioral components in FST are gender-dependent. The gender discrepancy related to rTMS should not be neglected in antidepressant treatment of rTMS.