Transcranial magnetic stimulation (TMS) is known to elicit a conditioning effect on cortical excitability. The purpose of this study was to investigate changes in cortical excitability induced by peripheral stimulation with differing frequency and stimulation site. A magnetic stimulator with a flat figure-eight coil was used for TMS and was performed on the left primary motor cortex. The electrical stimulation and magnetic stimulation were used in peripheral stimulation and the stimulus sites were the right and left supination of the forearm. Peripheral stimulation was performed at a stimulus frequency of 1 Hz or 10 Hz. Alterations of cortical excitability induced by peripheral stimulation were evaluated by comparing the mean of the motor evoked potential amplitude elicited by TMS each before and after peripheral stimulation. We found that cortical excitability varied according to the stimulation site and frequency in both the electrical and magnetic stimulation over the forearm. The inhibition of cortical excitability was observed in both 1 Hz electrical and magnetic stimulation over the right forearm. In contrast, the facilitation of cortical excitability was observed at 1 Hz electrical and magnetic stimulation over the left forearm, and it was confirmed for both the right and left forearms at 10 Hz electrical and magnetic stimulation. Moreover, regarding the alteration of cortical excitability induced by peripheral stimulation, it was confirmed that magnetic stimulation has more the significant difference than electrical stimulation. We suggest that peripheral stimulation by electrical and magnetic stimulation have a similar effect to TMS, and can induce both facilitation and inhibition of cortical excitability. Moreover, in the case of peripheral stimulation of the same stimulus frequency, we expect that the magnetic stimulation has more the significant effect than electrical stimulation to cortical excitability.