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Heart rate variability (HRV) and performance response during emergency flight maneuvers were analyzed. Two expert pilots (ages 35 and 33) and two rookie pilots (ages 25) from the Portuguese Air Force participated in this case–control report study. Participants had to complete the following emergency protocols in a flight simulator: (1) take-off engine failure, (2) flight engine failure close to the base, (3) flight engine failure far away from the base, and (4) alternator failure. The HRV was collected during all these maneuvers, as well as the performance data (the time it took to go through the emergency protocol and the subjective information from the flight simulator operator). Results regarding autonomic modulation showed a higher sympathetic response during the emergency maneuvers when compared to baseline. In some cases, there was also a higher sympathetic response during the emergency maneuvers when compared with the take-off protocol. Regarding performance data, the expert pilots accomplished the missions in less time than the rookie pilots. Autonomic modulation measured from HRV through portable devices can easily relay important information. This information is relevant since characterizing these maneuvers can provide helpful information to design training strategies to improve those psychophysiological responses.