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Purpose This paper aims to design the fractional order sliding mode controller for highly maneuverable remote piloted unmanned aircraft with time-varying delays. Design/methodology/approach With the assumption that the time-varying delays are bounded and identical for different outputs, an observer-based control technique is implied which reformulates the state variables based on the system model and delayed outputs. The estimated state variables are fed as feedback into the controller. Based on the delayed output observer, a fractional order sliding mode controller is designed. Further, the stability of the closed-loop system is analyzed and asymptotical convergence is realized using Lyapunov–Razumikhin theorem. Findings The simulation is done in Matlab and Simulink. The parametric variations and trajectory tracking results are illustrated which looks propitious. Practical implications In practical operation, measurement signal is often delayed, which significantly degrade the control performance or even disturb the stability. It is emphasized to choose attitude as the evaluation indicator for unmanned aerial vehicle time delay. Originality/value A novel fractional order sliding mode control technique is designed to enhance the trajectory tracking, thus autonomous flight performance, of the aircraft system. Also, the main idea behind this novel procedure is formulated for minimizing the parametric variations in presence of time delays.