The present study investigates the cerebral effects of chronic occupational stress and its possible reversibility. Forty-eight patients with occupational exhaustion syndrome (29 women) and 80 controls (47 women) underwent structural magnetic resonance imaging (MRI) and neuropsychological testing. Forty-four participants (25 patients, 19 controls) also completed a second MRI scan after 1–2 years. Only patients received cognitive therapy. The stressed group at intake had reduced thickness in the right prefrontal cortex (PFC) and left superior temporal gyrus (STG), enlarged amygdala volumes, and reduced caudate volumes. Except for the caudate volume, these abnormalities were more pronounced in females. They were all related to perceived stress, which was similar for both genders. Thickness of the PFC also correlated with an impaired ability to down-modulate negative emotions. Thinning of PFC and reduction of caudate volume normalized in the follow-up. The amygdala enlargement and the left STG thinning remained. Longitudinal changes were not detected among controls. Chronic occupational stress was associated with partially reversible structural abnormalities in key regions for stress processing. These changes were dynamically correlated with the degree of perceived stress, highlighting a possible causal link. They seem more pronounced in women, and could be a substrate for an increased cerebral vulnerability to stress-related psychiatric disorders.