Purpose – The aim of this paper is to present a research framework to investigate the behaviour of a Special Purpose Entity (SPE), i.e. a temporary project company, in the delivery of a megaproject, and, particularly uncover critical factors affecting the megaproject performance. Design/methodology/approach – The framework adopts a systemic knowledge-based perspective to construct the complex network of variables of the project governing system coordinated by the SPE. Fuzzy Cognitive Maps (FCMs) are used to elicit knowledge from expert and identify concepts and relationships associated to the variables of the SPE project governing system. Several scenarios are generated by performing FCM simulation. Originality/value –The proposed research framework allows dealing with the particular nature of uniqueness and complexity of infrastructure megaprojects by adopting a “case-based systemic” research approach to the study of the SPE and its project governing system that does not simplify, but rather preserves these project characteristics, and, in the same time, takes into account environment and context factors. Practical implications – The simulation output has showed that the contractor(s) technical capability, the SPE project management and planning capability and the SPE technical capability are important variables of the SPE governing system which influence project performance. Because of its flexibility, the framework can be used to model the project governing system coordinated by the SPE at different stages of the megaproject lifecycle, thus identifying the more important features and functions of the different SPE configurations.