North Korean Defectors (NKDs) are known to experience multiple psychological symptoms such depression and anxiety. Heart rate variability (HRV) has been implicated in various psychiatric disorders, including posttraumatic stress disorder (PTSD) and depression. No studies have prospectively evaluated HRV parameters in NKDs. We recruited 34 NKDs (2 men, 32 women; age range 25-58 years) who were diagnosed with major depressive disorder. We evaluated psychiatric symptoms using the Korean version of the Hamilton Depression Rating Scale (HDRS), Montgomery-Asberg Depression Rating Scale, and PTSD checklist civilian version. We also performed HRV measurements before and after 12 weeks of antidepressant treatment. In the baseline, HDRS item 14 and 15 showed statistically significant positive correlation with LF/HF ratio. At the endpoint, HDRS item 5 and 8 were found to have positive correlations with some HRV parameters. We found that the sum of fatigue-related HDRS symptoms scores (number 7 and 13) showed significant positive correlation with LF. HDRS total scores also showed significant positive correlations with LF and HF. When the severity of depression was decreased and only the PTSD symptoms persisted at the endpoint, the relationships between HRV and clinical measures were more clearly revealed. This study shows the possibility of using HRV as an objective neurobiological index of autonomic nervous system disorder and reaction to stress in NKDs.