In this work, the Uncertainty and Disturbance Estimation (UDE) approach is employed for the design of a robust flight controller for high performance aircraft. The UDE estimated uncertainty is used to robustify an input–output linearization-based controller designed for nominal system. The UDE theory employing a first-order filter and α-filter is used for the estimation of the composite uncertainty. To address the issue of output derivatives, an observer which too employs the UDE estimated uncertainties for the purpose of robustness is designed. Closed-loop stability for the overall controller-observer system is established. Uncertainties and disturbances in terms of parametric variations, wind gust, unmodeled actuator dynamics and measurement noise are considered to evaluate and compare performances of the two filter-based designs. Further, a performance comparison with some of the existing designs is carried out and the results are presented to demonstrate the efficacy of the proposed work. A notable feature of the proposed design is that the approach neither requires an accurate plant model nor any information about the uncertainties and disturbances.