The field of psychodynamic psychotherapy would benefit from a comprehensive model that integrates its constructs with neurobiology. Research on the autonomic nervous system activity during the psychotherapeutic process is necessary because it is key in affective experiences and defensive behavior. The current case study reports physiological findings on heart rate dynamics in a patient suffering from panic disorder during two therapeutic sessions in which we used Davanloo's Intensive Short-term Dynamic Psychotherapy. We looked at various metrics of heart rate variability during the therapeutic process leading to breakthrough of unconscious feelings. The measurements included sympathetic and parasympathetic indices, vagal tone, and their responses. Our results suggest that the sympathetic system activates during defensive responses associated with anxiety and during the passage of unconscious-aggressive impulses. Following the experience of unconscious guilt, there is an increased vagal tone corresponding to the phase of reunification with the attachment figure. Findings are discussed integrating developmental neurobiology and clinical psychodynamics.