Posttraumatic stress disorder (PTSD), which is caused by a major traumatic event, has been associated with autonomic nervous function. However, there have been few explorations of measuring biological stress in the victims\' family members who have been indirectly exposed to the disaster. Therefore, this longitudinal study examined the heart rate variability (HRV) of the family members of victims of the Sewol ferry disaster. We recruited 112 family members of victims 18 months after the disaster. Sixty-seven participants were revisited at the 30 months postdisaster time point. HRV and psychiatric symptoms including PTSD, depression and anxiety were evaluated at each time point. Participants with PTSD had a higher low frequency to high frequency ratio (LF:HF ratio) than those without PTSD. Logistic regression analysis showed that the LF:HF ratio at 18 months postdisaster was associated with a PTSD diagnosis at 30 months postdisaster. These results suggest that disrupted autonomic nervous system functioning for longer than a year after trauma exposure contributes to predicting PTSD vulnerability. Our finding may contribute to understand neurophysiologic mechanisms underlying secondary traumatic stress. Future studies will be needed to clarify the interaction between autonomic regulation and trauma exposure.