In this paper, a novel control scheme for the flexible air-breathing hypersonic vehicle (FAHV) using adaptive interval type-2 fuzzy logic system (AIT2-FLS) is proposed to reduce the side effects of measurement noises in the velocity channel and altitude channel as well as flexible dynamics in real applications. After input-output linearization of the longitudinal model of FAHV, the dynamic inversion controller is formulated to track the reference commands based on state feedback. The AIT2-FLS is further developed to deal with the model uncertainties and input errors. Besides, the state estimator is applied to estimate the true values of the corrupted outputs. The stability characteristics of both the controller and the state estimator are analyzed. The whole control scheme is finally obtained through combining the controller and the state estimator based on the separation principle. Simulation results demonstrate the robustness of our proposed control scheme against measurement noises and flexibilities.