This study is concerned with the augmented fixed-time observer based adaptive super-twisting cruise control for flexible air-breathing hypersonic vehicles (FAHVs). First, the input–output linearisation technique is employed to derive a control oriented FAHV dynamic model. Then, a super-twisting controller is designed to track the reference velocity and altitude commands when faced with various uncertainties and disturbances. In addition, a novel gain adaptation law is constructed as a supplement of the super-twisting controller to avoid overestimating the values of controller gains. The adaptation law keeps the controller gains adapting dynamically to guarantee the finite-time convergence of sliding variables in the presence of disturbances with unknown boundaries. Moreover, augmented fixed-time observers are designed to estimate the true values of measured states and filter out high-frequency sensor noises. Thus, the fixed convergence time of these observers is achieved independently of initial estimation errors. Finally, the augmented fixed-time observers and adaptive super-twisting controller are combined together to ensure the superior tracking performances of FAHVs under the effects of uncertainties, disturbances, and measurement noises.