Empathy is a multidimensional construct consisting of cognitive (inferring mental states) and emotional (empathic concern) components. Emotional empathy is severely impaired in individuals affected by Post-Traumatic Stress Disorder (PTSD). Here, we investigated the neural correlates of such an emotional empathy dysfunction to shed light on the neural circuitry responsible for the social and emotional dysfunction in PTSD. We asked a group of PTSD and a group of healthy controls to solve a Multifaceted Empathy Test, measuring both cognitive and emotional empathy, and investigated the functional connectivity of the cortical areas involved in solving the test. The results revealed that, in healthy individuals, increased neural activity in the frontal cortex modulates activity in the insula while subjects perform the emotional empathy task; whereas, in individuals affected by PTSD, increased activity in limbic regions such the insula and the amygdala modulates activity in the frontal cortex while performing the emotional empathy task. These findings suggest that the lack of cortical top-down control of the frontal cortex on the limbic system in PTSD during empathic processing may explain the emotional and social difficulties experienced by individuals suffering from PTSD.