Training assessment is usually done by evaluating information derived from instructor's supervision related to the pilot's operational performance and behavior. However, this approach lacks objective measures, especially regarding the pilots' mental states while accomplishing the flight training tasks. The study therefore aimed at developing and testing a method for gathering and analyzing in real-time pilots' brain activity and skin conductance to improve the training evaluation. In this regard, Novice pilots' neurophysiological signals were acquired throughout multi-crew training sessions. The results demonstrated how the methodology proposed was able to endow real-time pilots' mental workload and arousal assessment for i) better evaluating training progress and operational behavior during the training session, and ii) for objectively comparing different training sessions.