In tandem with the fast-growing demand for Unmanned Aerial Vehicles (UAVs) for surveillance and reconnaissance, advanced controllers for these critical systems are needed. This paper proposes a flight dynamics controller design that considers various uncertainties for the Hydra Technologies UAS-S4 Ehécatl. In order to be realistic, in addition to flight dynamics nonlinearities, three main sources of uncertainties are considered, as those caused by unknown controller’s parameters, modeling errors, and external disturbances. A Robust adaptive fuzzy logic controller is designed, in charge of nonlinear flight dynamics in presence of a variety of uncertainties. The nonlinear flight dynamics is modeled based on the Takagi-Sugeno method relying on the soft association of local linear models. Since this controller is model-based, an optimal reference model is defined, which is stabilised by the Linear Quadratic Regulator procedure. A fuzzy logic controller is then designed for the nonlinear model. Lastly, with the aim to handle the uncertainties, the gains of the fuzzy controller are reconfigured, and are continuously adjusted by Lyapunov-based robust adaptive laws. The performance of the UAS-S4 Robust adaptive fuzzy logic controller is evaluated in terms of lateral and longitudinal flight dynamics stabilisation, and the reference model state variables tracking under various uncertainties.