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Aggression is highly prevalent in borderline personality disorder (BPD). Previous studies have identified specific biobehavioral mechanisms underlying aggression in BPD, threat sensitivity being among them. We composited the mechanism-based anti-aggression psychotherapy (MAAP) in order to target these specific mechanisms, and MAAP was found to be superior to non-specific supportive psychotherapy (NSSP) in reducing aggressive behavior. In the present study, we investigated whether underlying brain mechanisms expected to be involved were affected by MAAP. To this end, n = 33 patients with BPD and overt aggressive behavior (n = 20 in MAAP, n = 13 in NSSP) and n = 25 healthy participants took part in a functional magnetic resonance imaging emotional face-matching task before and after treatment, or at a similar time interval for controls. Overt aggressive behavior was assessed using the overt aggression scale, modified. Results showed a decrease in amygdala activation in response to facial stimuli after MAAP, whereas an increase in amygdala activation was found after NSSP. Furthermore, in the MAAP group, connectivity between amygdala and dorsomedial prefrontal cortex increased from pre- to post-treatment compared to the NSSP group. Hence, the results suggest an impact of MAAP on brain mechanisms underlying the salience circuit in response to threat cues.