This study was conducted to compare the effects of low frequency repetitive transcranial magnetic stimulation (LF-rTMS) and high frequency repetitive transcranial magnetic stimulation (HF-rTMS) on upper limb function in stroke patients with acute stage. A total of 40 subjects were randomly assigned 20 each to the LF(1Hz)-rTMS group and the HF(10Hz)-rTMS group, and all subjects received intervention for 20 minutes a day, 5 times a week, for 2 consecutive weeks. The subjects" upper limb function was evaluated using the Wolf Motor Function Test (WMFT), Fugl-Meyer Assessment (FMA), Box and Block Test (BBT), and Jebsen-Taylor Hand Function Test (JTHFT). As a result of this study, there were significant differences between before and after intervention in WMFT and FMA in the LF-rTMS group (p < 0.05). In the HF-rTMS group, there was a significant difference between before and after the intervention in FMA, and there was also a significant difference between before intervention and follow up test (p < 0.01). There were no significant differences between groups in all dependent variables (p > 0.05). These suggest that LF-rTMS and HF-rTMS applied to the primary motor cortex had a positive effect on upper limb function in stroke patients with acute stage, but there was no significant difference in the effect between the two.