In this article, a robust discrete-time fractional-order tracking control scheme based on a discrete-time disturbance observer (DTDO) is proposed for an unmanned aerial vehicle (UAV) system in the presence of unknown bounded variation disturbances. A DTDO is first constructed to estimate the unknown bounded disturbance. On the basis of the output of the DTDO and the discrete-time fractional-order theories, a robust discrete-time fractional-order control scheme is then designed by using the backstepping control technique for a discrete-time UAV system with disturbances. The proposed control scheme is expected to guarantee the stability of the closed-loop system with all system signals bounded. Finally, numerical simulations are conducted to demonstrate the effectiveness of the proposed control scheme.