The aim of the present study was to investigate the relationship between resting heart rate variability (HRV) and cognitive functions during threat of shock. A Continuous Performance Task and a Working Memory Task were used to measure cognitive functions. Sixty-five male participants from the Royal Norwegian Navy participated. HRV was measured during baseline, test conditions and recovery. Participants were randomly assigned into non-threat and threat groups. Based on the median split of the high frequency (HF) spectral power, groups were divided into two additional groups. Overall, the high HRV participants showed superior performance on cognitive tasks independent of non-threat or threat conditions. During threat condition the low HRV group showed improved performance. Thus, individuals with high HRV were more stress tolerant and resilient in the face of environmental changes. The results from the study might have implications with regard to performance in operational settings, but also for other fields of psychological research such as individual differences, anxiety and coping.