Medical personnel often experience stress when responding to a medical emergency. A known stress-response is a measurable reduction in heart rate variability. It is currently unknown if crisis simulation can elicit the same stress response as real clinical emergencies. We aim to compare heart rate variability changes amongst medical trainees during simulated and real medical emergencies. We performed a single center prospective observational study, enrolling 19 resident physicians. Heart rate variability was measured in real time, using a 2-lead heart rate monitor (Bodyguard 2, Firstbeat Technologies Ltd) worn during 24 h critical care call shifts. Data was collected at baseline, during crisis simulation and when responding to medical emergencies. 57 observations were made to compare participant's heart rate variability. Each heart rate variability metric changed as expected in response to stress. Statistically significant differences were observed between baseline and simulated medical emergencies in Standard Deviation of the N-N interval (SDNN), Root mean square standard deviation of the N-N interval (RMSSD), Percentage of successive R-R intervals that differ by more than 50 ms (PNN50), Low Frequency (LF) and Low Frequency: High Frequency ratios (LF:HF). No statistically significant differences between simulated and real medical emergencies were identified in any heart rate variability metrics. We have shown using objective results, that simulation can elicit the same psychophysiological response as actual medical emergencies. Therefore, simulation may represent a reasonable way to practice not only essential skills in a safe environment but has the additional benefit of creating a realistic, physiological response in medical trainees.