High-speed UAV flight control is challenged by unknown external aerodynamic disturbances and internal system variations due to complex aerodynamic configuration, propellant consumption, the center of gravity movement, and possible actuator failures. Redundant aerodynamic control effectors and engine inlet control mechanisms are exploited/blended to maintain adequate force/moment control to satisfy flight control reliability requirements. A control allocation (CA) mixing matrix is an essential element of the redundancy design in addressing fault tolerance capabilities. This paper employs an Intelligent Flight Controller (IFC) implemented in an adaptive control augmentation fashion to assist the UAV’s primary Nonlinear Dynamic Inversion (NDI) controller in restoring aircraft stability and command following objective when subjected to effector performance degradation, including failures. Through a blended design between optimal control modification (OCM) and derivative-free model reference adaptive control (DF-MRAC), the IFC offers performance consistency in comparison to traditional MRAC. The proposed IFC framework has demonstrated its effectiveness in assisting the baseline NDI flight control system to maintain its mission subjected to actuator’s failures (via an implicit automatic CA ‘re-distributing’ action). Furthermore, the IFC also works well with any existing onboard CA algorithm in dealing with effector failures without requiring restructuring of the CA blending matrix. It therefore deserves consideration for application to future high Mach UAVs.