The aim of the present study was to examine the effects of high and low frequency repetitive transcranial magnetic stimulation on motor cortical excitability and the balance function in subacute stroke patients. Twenty-four subjects were randomly assigned to either the high frequency (HF) rTMS group, or the low frequency (LF) rTMS group, with 12 subjects each. All subjects received routine physical therapy. In addition, both groups performed a total of 20 sessions of rTMS for 20 minutes, once a day, 5 times per week, for a 4-week period. In the HF rTMS group, 10 Hz rTMS was applied daily to the hotspot of the lesional hemisphere; and in the LF rTMS group, 1 Hz rTMS was applied daily to the hotspot of the nonlesional hemisphere. Motor cortex excitability was determined by motor evoked potentials, and the balance function was evaluated by use of the Balance Index (BI) and the Berg Balance Scale (BBS), before and after the intervention. The change rate in the value of each variable differed significantly between the two groups (p<0.05). Furthermore, significant differences were observed between all post-test variables of the two groups (p<0.05). In the HF rTMS, significant differences were found in all the pre- and post-test variables (p<0.05). On the other hand, in the LF rTMS, significant difference was observed only between the pre- and post-test results of BI and BBS (p<0.05). The findings demonstrate that HF rTMS can be more helpful in improving the motor cortical excitability and balance function of patients with subacute stroke treatment than LF rTMS, and that it may be used as a practical adjunct to routine rehabilitation.