The autonomic nervous system (ANS) functioning has been proposed as a relevant method to characterize the therapeutic needs of intimate partner violence (IPV) perpetrators. Nevertheless, research has neglected the influence of the ANS on socio‐affective functions in this population. The aim of the present study was to analyze the psychophysiological activity of IPV perpetrators (n = 52) compared to controls (n = 46) following an empathic induction task, performed through negative emotion‐eliciting videos. We employed two general ANS markers (heart rate [HR] and respiratory rate [RR]), two sympathetic‐related indexes (pre‐ejection period [PEP] and skin conductance level [SCL]) and a parasympathetic biomarker (respiratory sinus arrhythmia [RSA]). Additionally, we explored the impact of psychophysiological activity on prosocial behavior using Hare's donation procedure. Compared to controls, IPV perpetrators reported lower HR and SCL following the task, as well as longer PEP, suggesting an attenuated sympathetic response to others' distress. No differences in the RSA response pattern were found, however, IPV perpetrators displayed lower overall RSA levels throughout the protocol, indicative of reduced parasympathetic activity. Besides, while no differences in prosocial performance were observed, greater sympathetic responses and overall parasympathetic activity predicted increased donations across the sample. Thus, a high sympathetic and parasympathetic activity might influence the occurrence of prosocial behavior. The present study provides further evidence supporting that IPV perpetrators cope differently with others' negative emotions. In line with this biopsychosocial perspective, insights are gained on the emotional processing of IPV perpetrators which, in turn, could contribute to improve IPV psychotherapeutic programs.