Reduced cardiac autonomic function is associated with increased risk of cardiovascular disease (CVD), with heart rate variability (HRV) providing an accessible index of cardiac autonomic function. HRV may provide a candidate physiological mechanism linking reduced cardiac autonomic function to increased risk for CVD in schizophrenia illness. This study examines whether HRV is also reduced in a community sample of treatment-seeking participants experiencing early psychosis (n = 48) compared to healthy volunteers (n = 48) and social anxiety control groups (n = 48) matched by gender and age. HRV was assessed during a five-minute interbeat interval recording at rest. Participants also completed self-report psychiatric symptom measures. Early psychosis participants showed significant reductions in HRV compared to social anxiety and healthy control groups. Reductions in HRV were also observed in early psychosis participants taking anticholinergic medications compared to both control groups taking cardio-benign medications or who were non-medicated. Lastly, whether or not early psychosis participants were taking anticholinergic medications was not associated with reductions in HRV. Findings provide preliminary evidence that early psychosis is associated with reduced HRV. This study supports further research with larger sample sizes to precisely determine the influence of anticholinergic drugs on HRV in early psychosis populations.