Reaction time (RT) is shortened when the response signal is preceded by a warning signal, a finding that has been attributed to response preparation during the foreperiod between the warning and response signals. Research suggests an increased excitability of cortical movement representations associated with response preparation during the foreperiod of a warned RT task (Davranche et al. in Eur J Neurosci 25:3766–3774, 2007). However when the foreperiod duration is short and constant, the motor evoked potential (MEP) amplitude elicited by transcranial magnetic stimulation (TMS) during the foreperiod is suppressed (Touge et al. in Clin Neurophysiol 111:1216–1226, 1998), suggesting a competing inhibitory process. Three experiments measured MEP amplitude and intracortical inhibition during the foreperiod of a warned RT task in which the response was a flexion of the right index finger. Experiments 1 and 2 measured short-interval intracortical inhibition (SICI) with paired TMS pulses separated by inter-stimulus intervals (ISIs) of 3 (SICI3) and 1.5 ms (SICI1.5), respectively. Experiment 3 measured long-interval intracortical inhibition (LICI) with paired TMS pulses with an ISI of 100 ms (LICI100). In all experiments MEP amplitude was smaller in the warned condition than in the unwarned condition. There was less SICI3 in the warned condition than in the unwarned condition (Experiment 1) whereas SICI1.5 was similar in both conditions (Experiment 2). There was less LICI100 in the warned condition than in the unwarned condition (Experiment 3). The intracortical inhibitory processes measured here cannot explain the suppression of MEP amplitude in the warned condition. We propose that the suppression of MEP amplitude is the result of an inhibitory mechanism, which acts on primary motor cortex to prevent premature response during the foreperiod.