This paper presents a novel nonfragile output tracking control scheme for flexible hypersonic air-breathing vehicles (HAVs). This problem is challenging due to the complex interactions between the aerodynamics, the propulsion system, and the structural dynamics. By utilizing the curve-fit and the least-squares methods, a new model for HAVs is established, and then converted into a linear parameter-varying system, in which the scheduling variables depend on a handful of meaningful states and parameters. With a specified reference model, a tracking error model is also proposed. The nonfragile output tracking controller is designed, which guarantees the tracking error dynamics to be robustly stable. Finally, simulation results are presented to show the effectiveness of the proposed control design scheme.