Heart rate variability (HRV) is considered an index of self-regulatory capacity, and trait compassion predicts healthy HRV and self-regulation. Compassion focused psychotherapy interventions have been shown to increase levels of compassion in the general population but no studies to date have examined if these interventions also increase HRV in a distressed clinical sample. The present study examined whether a 12-week compassion focused therapy intervention administered in group format would improve resting HRV and impact HRV reactivity during self-critical writing and self-compassion writing tasks administered before and after the intervention. A total of 31 participants in a university counseling center completed the intervention and HRV assessments. Resting HRV did not significantly change over the course of the intervention in the overall sample. Only those who showed a reliable increase in self-compassion also had a significant increase in resting HRV post-intervention. Additionally, the self-critical writing task was associated with a significant decrease in HRV, with HRV staying low during self-compassionate writing and then significantly increasing during recovery. Reliable change in self-compassion predicted increased HRV reactivity to self-critical and self-compassion writing tasks following the intervention, indicating greater engagement with the task. Findings support the idea that increased self-compassion increases HRV reactivity and potentially strengthens ability to engage with difficult emotions in psychotherapy.