Men and women show important differences in clinical conditions in which deficits in cognitive control are implicated. We used functional magnetic resonance imaging to examine gender differences in the neural processes of cognitive control during a stop-signal task. We observed greater activation in men, compared to women, in a wide array of cortical and sub-cortical areas, during stop success (SS) as compared to stop error (SE). Conversely, women showed greater regional brain activation during SE > SS, compared to men. Furthermore, compared to women, men engaged the right inferior parietal lobule to a greater extent during post-SE go compared to post-go go trials. Women engaged greater posterior cingulate cortical activation than men during post-SS slowing in go trial reaction time (RT) but did not differ during post-SE slowing in go trial RT. These findings extended our previous results of gender differences in regional brain activation during response inhibition. The results may have clinical implications by, for instance, helping initiate studies to understand why women are more vulnerable to depression while men are more vulnerable to impulse control disorders.