In a therapeutic environment a proper regulation of the empathic response strengthens the patient-therapist relationship. Thus, it is important that psychotherapists constantly regulate their own perspective and emotions to better understand the other’s affective state. We compared the empathic abilities of a group of 52 psychotherapists with a group of 92 non-psychotherapists and found psychometric differences. Psychotherapists showed greater scores in Fantasy and Perspective Taking, both cognitive empathy constructs, and lower scores in the use of expressive suppression, an emotional regulation strategy that hampers the empathic response, suggesting that psychotherapists exert top-down processes that influence their empathic response. In addition, the expected sex differences in empathic concern and expressive suppression were only present in the non-psychotherapist group. To see if such psychometric differences were related to a distinctive functional organization of brain networks, we contrasted the resting state functional connectivity of empathy-related brain regions between a group of 18 experienced psychotherapists and a group of 18 non-psychotherapists. Psychotherapists showed greater functional connectivity between the left anterior insula and the dorsomedial prefrontal cortex, and less connectivity between rostral anterior cingulate cortex and the orbito prefrontal cortex. Both associations correlated with Perspective Taking scores. Considering that the psychometric differences between groups were in the cognitive domain and that the functional connectivity associations involve areas related to cognitive regulation processes, these results suggest a relationship between the functional brain organization of psychotherapists and the cognitive regulation of their empathic response.