This paper proposes a fault tolerant control scheme based on an unknown input observer for a wind turbine system subject to an actuator fault and disturbance. Firstly, an unknown input observer for state estimation and fault detection using a linear parameter varying model is developed. By solving linear matrix inequalities (LMIs) and linear matrix equalities (LMEs), the gains of the unknown input observer are obtained. The convergence of the unknown input observer is also analysed with Lyapunov theory. Secondly, using fault estimation, an active fault tolerant controller is applied to a wind turbine system. Finally, a simulation of a wind turbine benchmark with an actuator fault is tested for the proposed method. The simulation results indicate that the proposed FTC scheme is efficient.