The present study aimed to investigate the effects of changes in motor-evoked potential (MEP) amplitude on short-latency afferent inhibition (SAI) and short-interval intracortical inhibition (SICI). MEPs in response to transcranial magnetic stimulation (TMS) of the left primary motor cortex were measured from the right first dorsal interosseous muscle of 10 healthy participants. SAI was evaluated by measuring MEPs in response to variable-intensity test TMS pulses delivered 22 ms following electrical stimulation of the right ulnar nerve (intensity fixed at the motor threshold). SICI was evaluated by pairing a constant conditioning TMS pulse [80% of resting motor threshold (RMT)] with a second variable-intensity TMS test pulse (interstimulus interval of 2 ms). The intensity of the test stimulus was set at 110, 115, 120, 125, or 130%RMT on a given trial. SAI was significantly reduced when evoked by a 125%RMT test TMS pulse compared with 110%RMT, and absent at 130%RMT. There was no significant difference in SICI at 110–130%RMT. Significant positive correlations were detected between the unconditioned and conditioned MEP amplitudes at both SAI and SICI. This study demonstrated that SAI and SICI are highly sensitive to the MEP amplitude and SAI decreases with increasing MEP amplitude, whereas SICI does not change. The different responses for SAI and SICI to the increasing MEP amplitude is interpreted as evidence that different inhibitory neural circuits may be involved in SAI and SICI.