The present study was aimed at deciphering whether the delay in choice reaction time (RT) and the silent period (SP) caused by transcranial magnetic stimulation (TMS) of the motor cortex in the ongoing electromyogram are due to the same physiological mechanism. To this end, the effect of TMS was studied in 6 healthy volunteers performing a between-hand choice RT task. Specific predictions were derived from a logic inspired from the “postponed stages” hypothesis (Pashler & Johnson, 1989). This logic predicts a correlation between SP duration and RT when the stimulated cortex is involved in the response, and a stronger correlation when the stimulation is delivered later during the RT interval. The effect of TMS on RT was twofold: At early stimulation times, the stimulation shortened the RT and this effect was independent of the involvement of the stimulated motor cortex in the subsequent response. At later stimulation times, TMS had a disruptive effect, provided that the stimulated cortex was involved in the response. When the stimulated cortex was involved in the response, there was a correlation between SP and RT; this correlation was stronger when the stimulation occurred later. In contrast, there was no correlation between these two variables when the stimulated cortex was not involved.