We measured fMRI signals in response to excitatory and inhibitory TMS modulations over the human primary motor cortex (M1) with TMS bursts of high (10- and 30-Hz) and low frequency (0.5-Hz) with a controlled TMS dosage over the 30-s interval, respectively. Excitatory and inhibitory modulations were evidenced by motor evoked potential changes. Significantly increased fMRI signal at M1 was only detected under excitatory high-frequency TMS but not during inhibitory low-frequency TMS. The supplementary motor area (SMA) had significant fMRI signal changes after both kinds of TMS. The topology of the activated M1 and SMA matched those during the voluntary movement.