This paper designs a fault-tolerant adaptive controller for air-breathing hypersonic vehicles (AHVs) subject to modelling parameter uncertainties, external disturbances, and actuator nonlinearities of saturation and backlash. The proposed adaptive control scheme is able to compensate the effects of actuator saturation by utilising the states of five auxiliary dynamic systems, which are driven by the differences between the nominal and saturated input signals. Additionally, the effects of control surfaces on the aerodynamic force and moment, which are commonly neglected by the existing adaptive control designs, can be well handled. Transient tracking performance is explicitly derived in terms of norms of the tracking errors. The final control scheme is obtained in a direct form, which makes its implementation more practical compared with other adaptive controllers for AHVs. The effectiveness of the proposed control scheme is demonstrated by numerical simulations.