Previous research indicated a need to improve pilot training with regard to understanding of autopilot logic and behavior, especially in non-routine situations. Therefore, we tested the effect of problem-based exploratory training on pilots’ understanding of autopilot functions. Using a moving-base flight simulator, general aviation pilots (n = 45) were trained to diagnose failures either without foreknowledge and guidance (exploratory group), without foreknowledge but with some guidance (exploratory-guidance group) or with foreknowledge and full guidance (control group). They subsequently performed six test scenarios in which their understanding of the effects of failures was tested by requiring them to deduce the failures and select autopilot modes that were still functioning. Those who received exploratory training with guidance were significantly more likely than the other groups to diagnose failures correctly. The exploratory training group also selected the most appropriate functioning autopilot modes significantly faster than the control group. The results suggest that exploratory training with an appropriate level of guidance is useful for gaining a practical understanding of autopilot logic and behavior. Exploratory training may help to improve transfer of training to operational practice, and prevent automation surprises and accidents.