The purpose of the current study was to investigate the effect of repetitive transcranial magnetic stimulation (rTMS) in conjunction with mirror therapy on the balance function of patients with sub-acute stroke hemiparesis. This study was conducted with 36 subjects who were diagnosed with a hemiparesis due to stroke. Participants in the experimental (19 members) and control groups (17 members) received rTMS and sham rTMS during 10 minute sessions each, which were carried out five days per week for four weeks. This was followed by the mirror therapy over 30 minute sessions, which were carried out five days per week for four weeks. Motor recovery was assessed by balance index, dynamic limits of stability, Berg balance scale, and time up go test. The change values of the balance index (−2.06 ± 1.99 versus −0.41 ± 1.11), dynamic limits of stability (3.68 ± 2.71 versus 1.17 ± 2.38), and time up go test (−7.05 ± 5.64 score versus −3.35 ± 5.30 score) were significantly higher in the experimental group than in the control group (p < 0.05). At post-test, balance index (4.08 ± 1.14 versus 5.09 ± 1.04), dynamic limits of stability (13.75 ± 0.60 versus 11.73 ± 3.53), and time up go test (23.89 ± 4.51 versus 28.82 ± 3.07) were significantly higher in the experimental group than in the control group (p <0.05). In the experimental group, significant differences were found in the pre- and post-test scores for the balance index, dynamic limits of stability, Berg balance scale, and time up go test (p < 0.01). In the control group, a significant difference was observed between the pre- and post-test only for the Berg balance scale and time up go test (p < 0.05). These findings demonstrate that the application of 1Hz rTMS in conjunction with mirror therapy can be helpful in improving the balance function of patients with sub-acute stroke hemiparesis, and this may be used as a practical adjunct to routine rehabilitation therapy.