A sliding mode corrector is presented for disturbance rejection in position sensing using relatively accurate velocity measurement. The corrector design is based on a robust second-order sliding mode (2-sliding mode), which makes the fusion of position and velocity on a sliding surface to reject disturbance. Even when the frequency bands of disturbance and actual position signal overlap, or large-magnitude disturbance exists, the corrector can still provide the accurate and smoothed estimate of position. The proposed corrector is applied to a jet UAV navigation and control. In the unmanned aerial vehicle (UAV) system, the disturbances exist in position and attitude measurements, and the uncertainties exist in the system dynamics. For the UAV trajectory tracking control, the system model is constructed in the earth-fixed frame, and the constructed model is fit for observer design to estimate system uncertainties. The control laws are designed according to the correction of position and attitude by the correctors and the estimation of system uncertainties by an existing observer. Finally, the flight experiment demonstrates the effectiveness of the proposed method.