High-frequency repetitive transcranial magnetic stimulation (rTMS) is widely used to improve motor function in stroke patients. However, the long-term effects of rTMS on disability and motor function are not clear. We investigated the effects of high-frequency rTMS administered within 1 month of stroke on disability and motor function 6 months after stroke onset. The study was conducted by an open-label longitudinal study, and were included 76 (38 rTMS and 38 control) subacute stroke patients. The rTMS group received 10 Hz stimulation over the primary motor cortex of the affected hemisphere for 10 days with a daily dose of 1000 pulses. The Korean version of the Modified Barthel Index (K-MBI), the Medical Research Council (MRC) scale for motor deficits in the affected arm, the Manual Function Test (MFT), and the Functional Ambulation Classification (FAC) were administered at baseline (within 1 month of stroke onset) and at 3 and 6 months after onset. The K-MBI, MRC scale, MFT, and FAC scores of both groups changed significantly over time (p < 0.001); however, the motor strength, hand function, FAC classification, and K-MBI scores of the rTMS and control groups did not differ. Our findings indicate that rTMS did not have a long-lasting effect (6 months after onset) on disability and motor function in patients with stroke.