The ability to stop ongoing motor responses in a split-second is a vital element of human cognitive control and flexibility that relies in large part on prefrontal cortex. We used the stop-signal paradigm to elucidate the engagement of primary motor cortex (M1) in inhibiting an ongoing voluntary motor response. The stop-signal paradigm taps the ability to flexibly countermand ongoing voluntary behavior upon presentation of a stop signal. We applied single-pulse TMS to M1 at several intervals following the stop signal to track the time course of excitability of the motor system related to generating and stopping a manual response. Electromyography recorded from the flexor pollicis brevis allowed quantification of the excitability of the corticospinal tract and the involvement of intracortical GABABergic circuits within M1, indexed respectively by the amplitude of the motor-evoked potential and the duration of the late part of the cortical silent period (SP). The results extend our knowledge of the neural basis of inhibitory control in three ways. First, the results revealed a dynamic interplay between response activation and stopping processes at M1 level during stop-signal inhibition of an ongoing response. Second, increased excitability of inhibitory interneurons that drives SP prolongation was evident as early as 134 msec following the instruction to stop. Third, this pattern was followed by a stop-related reduction of corticospinal excitability implemented around 180 after the stop signal. These findings point to the recruitment of GABABergic intracortical inhibitory circuits within M1 in stop-signal inhibition and support the notion of stopping as an active act of control.