Repetitive transcranial magnetic stimulation (rTMS) has been studied increasingly in recent years to determine whether it has a therapeutic benefit on recovery after stroke. However, the underlying mechanisms of rTMS in stroke recovery remain unclear. Here, we evaluated the effect of rTMS on functional recovery and its underlying mechanism by assessing proteins associated with neural plasticity and anti-apoptosis in the peri-lesional area using a subacute cerebral ischemic rat model. Twenty cerebral ischemic rats were randomly assigned to the rTMS or the sham group at post-op day 4. A total of 3,500 impulses with 10 Hz frequency were applied to ipsilesional cortex over a 2-week period. Functional outcome was measured before (post-op day 4) and after rTMS (post-op day 18). The rTMS group showed more functional improvement on the beam balance test and had stronger Bcl-2 and weaker Bax expression on immunohistochemistry compared with the sham group. The expression of NMDA and MAP-2 showed no significant difference between the two groups. These results suggest that rTMS in subacute cerebral ischemia has a therapeutic effect on functional recovery and is associated with an anti-apoptotic mechanism in the peri-ischemic area rather than with neural plasticity.