Previous studies have shown that intracortical inhibition (ICI) plays an important role in shaping the output from primary motor cortex (M1). This study explored the muscle specificity and temporal modulation of ICI during the performance of a phasic index finger flexion task. Fifteen subjects were asked to rest their dominant hand on a computer mouse and depress the mouse button using their index finger in time with a 1-Hz auditory metronome, while keeping the rest of their hand as relaxed as possible. Responses to single- and paired-pulse transcranial magnetic stimulation were recorded from the first dorsal interosseous (FDI) and abductor pollicis brevis (APB) muscles while subjects were at rest and during "on" and "off" phases of the task. For FDI during the on phase, motor evoked potential (MEP) amplitude and pretrigger EMG increased and ICI decreased, as expected. This pattern of modulation was also observed for APB in seven subjects. The remaining eight subjects demonstrated a decrease in MEP amplitude and increase in ICI for APB during the on phase. This was associated with significantly less APB activation during the on phase. These findings suggest that an increase in ICI and decrease in corticospinal excitability can prevent unwanted muscle activation in a muscle-specific, temporally modulated manner.