This paper discusses the challenge of modeling in-flight startle causality as a precursor to enabling the development of suitable mitigating flight training paradigms. The article presents an overview of aviation human factors and their depiction in fuzzy cognitive maps (FCMs), based on the Human Factors Analysis and Classification System (HFACS) framework. The approach exemplifies system modeling with agents (causal factors), which showcase the problem space’s characteristics as fuzzy cognitive map elements (concepts). The FCM prototype enables four essential functions: explanatory, predictive, reflective, and strategic. This utility of fuzzy cognitive maps is due to their flexibility, objective representation, and effectiveness at capturing a broad understanding of a highly dynamic construct. Such dynamism is true of in-flight startle causality. On the other hand, FCMs can help to highlight potential distortions and limitations of use case representation to enhance future flight training paradigms.