Purpose: Individuals with eating disorder (ED) are at an increased risk of cardiac arrhythmias due to cardiac dysautonomia, which may be exacerbated if depression is also present. The aim of the study was to use heart rate analysis as a marker for cardiac dysautonomia in patients with eating disorders and depression as a comorbidity. Methods: Clinical data, including presence of depression, was obtained from all participants. A three-lead ECG was used to determine interbeat intervals, and these were analyzed using time domain, frequency domain, and nonlinear heart rate variability measures. Results: Thirty ED patients and 44 healthy controls participated in the research. The presence of depression was associated with additional decreased time domain (RMSSD 36.8 ± 26 vs. 22.9 ± 12.3; p < 0.05), frequency domain (HF power 788 ± 1075 vs. 279 ± 261; p < 0.05), and nonlinear domain (DFAα2 0.82 ± 0.1 vs. 0.97 ± 0.1; p < 0.01) which results in the ED group compared to patients with no depression. Conclusions: The presence of depression in ED patients decreased HRV even further compared to the non-depressed patient group and controls, suggesting that higher vigilance and a holistic treatment approach may be required for these patients to avoid cardiac arrhythmia complications.