Bimanual coordination tasks form an essential part of our behaviour. One brain region thought to be involved in bimanual coordination is the supplementary motor area (SMA). We used repetitive transcranial magnetic stimulation (rTMS) at 1 Hz for 5 min to create a temporary virtual lesion of the rostral portion of the human SMA immediately prior to performance of a goal-directed bimanual coordination task. In two control conditions, participants underwent sham stimulation or stimulation over the primary motor cortex (MI). The experimental task was to open a drawer with the left hand, catch a ball with the right hand, and reinsert the ball into the drawer through an aperture just big enough for the ball to pass through, again with the right hand. Hence, the actions of one hand depend upon the actions of the other. We calculated time intervals between the successive component actions of one hand (unimanual intervals) and actions of both hands (bimanual intervals) and analyzed these intervals separately. Interestingly, none of the unimanual intervals were affected by the rTMS, but the variability of a critical bimanual interval—the time between the left hand opening the drawer and the right hand starting to move to catch the ball—was increased by rTMS over the rostral parts of the SMA. No such effect was seen following rTMS over MI or after sham rTMS. Our results suggest that the rostral parts of the SMA play an important role in aspects of functional bimanual tasks, which involve tight temporal coordination between different motor actions of the two hands.