This paper is concerned with the state predictor based adaptive second-order sliding mode trajectory tracking control for flexible air-breathing hypersonic vehicles with measurement noises. Input-output linearization theory is first utilized to obtain the control oriented model. Then, the second-order sliding mode controller is designed to track the desired velocity and altitude. A novel gain adaptation law is proposed thereafter to achieve the non-overestimating values of controller gains, keeping the controller gains adapt dynamically to ensure the finite-time convergences of sliding variables in the presence of unknown uncertainties and disturbances. In addition, a state predictor is developed to estimate the true values of the velocity and altitude with measurement noises. Finally, the state predictor and adaptive second-order sliding mode controller are combined together to ensure the superior performance of the tracking control system under the influences of uncertainties, disturbances and measurement noises.