In aviation, mental workload and stress are two major factors that can considerably impact a pilot’s flight performance and decisions. Their consequences can be even more dramatic in single-pilot aircraft or with the forthcoming single-pilot operations where the pilot will fly alone and will not be able to be assisted in case of difficulty. An accurate and automatic monitoring of the pilot’s mental state could help to prevent the potentially dangerous effects of an excess mental workload and stress. For example, some tasks could be allocated to automation or to a ground-based flight crew if a mental overload or significant stress is detected. In the current study, the brain activity of 20 private pilots was recorded with a fNIRS device during two realistic flight simulator scenarios. The mental workload was manipulated with the added difficulty of a secondary task and stress was induced by a social stressor. Our results confirmed the sensitivity of the fNIRS readings to variations in the mental workload, with increased HbO2 concentration in regions of the executive control network (ECN), in particular in the dorsolateral prefrontal cortex and in lateral parietal regions, when the difficulty of the secondary task was high. The social stressor also triggered an HbO2 increase in the ECN, especially when it was combined with high mental workload. This latter result suggests that mental workload and stress together can have cumulative effects, and coping with both factors is possible at the expense of an extra recruitment of the ECN. Finally, results also revealed a time-on-task effect, with a progressive reduction of the HbO2 signal in the ECN during the flight scenario, suggesting that these regions are sensitive to short term habituation to the tasks. Overall, fNIRS efficiently indexed mental load, stress, and practice effects.