Suppressed heart rate variability (HRV) has been found in a number of psychiatric conditions, including schizophrenia and autism. HRV is a potential biomarker of altered autonomic functioning that can predict future physiological and cognitive health. Understanding the HRV profiles that are unique to each condition will assist in generating predictive models of health. In the current study, we directly compared 12 adults with schizophrenia, 25 adults with autism, and 27 neurotypical controls on their HRV profiles. HRV was measured using an electrocardiogram (ECG) channel as part of a larger electroencephalography (EEG) study. All participants also completed the UCLA Loneliness Questionnaire as a measure of social stress. We found that the adults with schizophrenia exhibited reduced variability in R-R peaks and lower low frequency power in the ECG trace compared to controls. The HRV in adults with autism was slightly suppressed compared to controls but not significantly so. Interestingly, the autism group reported feeling lonelier than the schizophrenia group, and HRV did not correlate with feelings of loneliness for any of the three groups. However, suppressed HRV was related to worse performance on neuropsychological tests of cognition in the schizophrenia group. Together, this suggests that autonomic functioning is more abnormal in schizophrenia than in autism and could be reflecting health factors that are unique to schizophrenia.