Many different types of aircraft designs have flight control systems (FCS) powered by hydraulic systems. With respect to the torques, moments, surface areas, and opposing forces to be acted upon, components introduce faults into the hydraulic system when these components are aging or degrading. The diagnostics of a hydraulically powered flight control actuation system (HPFCAS) rely on the faults produced within the subsystem components as well as the entire system’s mechanism itself. In this paper, a model for an HPFCAS is developed to analyze faults where the HPFCAS was approached as a system of systems (SOS). The identified faults were injected into the system. It is established that some of the faults from the different subsystems had similar characteristic effects and were propagated with attendant consequences. For instance, a measured decrease in the pressure value is observed because of the decrease in the pump speed. A similar characteristic is observed if there is leakage on the line or if there is a clogging valve. These form complex integrated responses in determining where the fault is coming from if only one component is analyzed since it involves components serving different subsystems. Results show that only models that can describe the real characteristics or attributes of the specific systems, due to their defined components, are sufficient for effective diagnostics. This is because the data obtained are more accurate at predicting the behavior of components.