BACKGROUND: Recently, high-frequency repetitive transcranial magnetic stimulation (HF-rTMS) and low-frequency rTMS (LF-rTMS) are reported to improve motor function significantly in chronic hemiparetic stroke patients. However, few studies have investigated the safety and efficacy of these rTMS modalities introduced during the early phase of stroke. The purpose of this study was to clarify the rTMS modality that is more beneficial for upper limb hemiparesis in the early phase of stroke using a randomized controlled trial. METHODS: Twenty-nine patients with a hemispheric stroke lesion in the early phase of stroke were examined. Patients were randomly assigned into 3 groups: the HF-rTMS group (10 Hz rTMS to the lesional hemisphere [n = 9]), the LF-rTMS group (1 Hz rTMS to the nonlesional hemisphere [n = 11]), and the sham stimulation group [n = 9]). Patients received sessions for 5 consecutive days. Grip strength and tapping frequency were assessed before and after the intervention. Motor improvement of the affected upper limb after intervention was compared among the 3 groups. RESULTS: All patients completed the 5-day protocol. Both the HF-rTMS and LF-rTMS groups had significant increases in both grip strength and tapping frequency. Comparison of the extent of improvement showed a more significant increase in grip strength and tapping frequency in the HF-rTMS group compared to the sham stimulation group (each P < .05), and no difference between the LF-rTMS group and the sham stimulation group. CONCLUSIONS: HF-rTMS applied to the lesional hemisphere in the early phase of stroke was more beneficial for motor improvement of the affected upper limb than LF-rTMS.