This paper addresses the design of attitude and airspeed controllers for a fixed wing unmanned aerial vehicle. An adaptive second order sliding mode control is proposed for improving performance under different operating conditions and is robust in presence of external disturbances. Moreover, this control does not require the knowledge of disturbance bounds and avoids overestimation of the control gains. Furthermore, in order to implement this controller, an extended observer is designed to estimate unmeasurable states as well as external disturbances. Additionally, sufficient conditions are given to guarantee the closed-loop stability of the observer based control. Finally, using a full 6 degree of freedom model, simulation results are obtained where the performance of the proposed method is compared against active disturbance rejection based on sliding mode control. •An observer based control for tracking desired trajectories for a fixed wing unmanned aerial vehicle is proposed.•This approach is robust under parametric uncertainties and external disturbances via an extended state observer.•Extended observers are used to estimate the state vector and external perturbations.•The adaptive second order sliding mode controller ensures finite time convergence and requires less control effort.•Stability analysis for the observer based control is given.