The ability to produce appropriate physiological and psychological responses to stressful situations depends on accurate recognition and appraisal of such situations. Such ability is also important for proper emotion regulation. A number of studies have suggested that the medial prefrontal cortex (mPFC) plays a significant role in emotion regulation, as well as in the control of physiological endpoints of emotion regulation such as the hypothalamic-pituitary-adrenal (HPA) axis and autonomic nervous system (ANS). Further, recent work has suggested that men and women may differ in these mechanisms of neural control of emotion regulation. Here, we examined the role of the human mPFC in self-report, ANS, and HPA stress reactivity by testing a group of participants with damage to this region (9 women and 9 men), a brain damaged comparison group (6 women and 6 men), and healthy comparison participants (27 women and 27 men) on an orthostatic challenge and the Trier Social Stress Test (TSST). The mPFC participants showed heightened self-reported stress in response to the TSST. In women, mPFC damage led to an increased cortisol response to the TSST. By contrast, in men, greater volume of mPFC damage was correlated with a decreased cortisol response. Finally, men with mPFC damage showed altered autonomic control of the heart (higher heart rate and lower high frequency heart rate variability) during an orthostatic challenge. These findings support the idea that the mPFC is involved in the regulation of physiological and psychological responses to stress and that this regulation may differ between men and women.