“Resonance mechanism” represents one important aspect of empathy, which includes emotional cue detection, facial mimicry (EMG) and a specific cortical response. The present research explored the convergence of these three different measures of affective empathy. Twenty students took part in the study. They were required to empathize with the situation by entering into the other person’s situation (four emotional face types: anger, fear, happiness, and neutral), and they were instructed to make a two-alternatives response (emotion; no emotion). A repeated Transcranial Magnetic Stimulation was used in order to produce a temporary inhibition of medial prefrontal cortex (MPFC). Findings support the hypothesis that there is a direct relationship between the emotional cue recognition, EMG facial response and prefrontal activity. Firstly, the two measures of facial expression detection and autonomic mimic reaction to emotional faces were systematically modulated in response to the MPFC inhibition. Secondly, medial prefrontal cortex was found to be related to facial cue detection and autonomic response, that is it was observed an impaired performance on both measures in case of inhibition of medial frontal cortex. Thirdly, this effect was reported in greater measure when negatively valenced stimuli (angry and fearful faces) were presented to the subjects. The present results showed a significant effect of MPFC on both cue detection and facial mimic, distinctly related to different emotional types.