Although both the presupplementary motor area (pre-SMA) and the right inferior frontal gyrus (rIFG) have been demonstrated to be critical for response inhibition, there is still considerable disagreement over the roles they play in the process. In the present study, we investigated the causal relations of the pre-SMA and the rIFG in a conditional stop-signal task by applying offline theta-burst transcranial magnetic stimulation. The task introduced a continue condition, which requires the same motor response as in a go trial but captures attention as in a stop trial. We found great individual differences in the amount of slowing on continue trials. Temporary suppression of pre-SMA activity prolonged the continue RT in participants who slowed little in response to continue trials, whereas disruption of the rIFG did not lead to significant changes in performance irrespective of the degree of slowing. Our results contribute to the understanding of the role of the pre-SMA by providing causal evidence that it is involved in response slowing on continue trials during conditional stopping, and it is likely that its efficiency in updating motor planning and reinitiating an inhibited response was associated with the amount of slowing.