In order to study neural systems which are involved in motor timing we used whole-brain functional resonance imaging while subjects performed a paced finger-tapping task (PFT) with their right index finger. During one condition, subjects were imaged while tapping in synchrony with tones separated by a constant interval (auditory synchronisation, AS), followed by tapping without the pacing stimulus (auditory continuation, AC). In another condition, subjects were imaged while tapping in synchrony with a visual stimulus presented at the same frequency as the tones (visual synchronisation, VS) followed by a tapping sequence without visual pacing (visual continuation, VC). The following main results were obtained: (1) tapping in the context of visual pacing was generally more variable than tapping in the context of auditory stimuli; (2) during all conditions, a fronto-parietal network was active including the dorsal lateral premotor cortex (dPMC), M1, S1, inferior parietal lobule (LPi), supplementary motor cortex (SMA), the right cerebellar hemisphere, and the paravermial region; (3) stronger activation in the bilateral ventral premotor cortex (vPMC), the left LPi, the SMA, the right inferior cerebellum, and the left thalamus during both auditory conditions (AS and AC) compared to the visual conditions (VS and VC); (4) stronger activation in the right superior cerebellum, the vermis, and the right LPi during the visual conditions (VS and VC); (5) similar activations for the AS and AC conditions; but (6) marked differences between the VS and VC conditions especially in the dorsal premotor cortex (dPMC) and LPi areas; and (7) finally, there were no activations in the auditory and visual cortices when the pacing stimuli were absent. These findings were taken as evidence for a general difference between the motor control modes operative during the auditory and visual conditions. Paced finger tapping in the context of auditory pacing stimuli relies more on brain structures subserving internal motor control while paced finger-tapping in the context of visual pacing stimuli relies on brain structures relying on the subserving processing or imagination of visual pacing stimuli.