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This article investigates the non-integer order model and the controller for aerodynamic load simulator system using fractional order adaptive fuzzy back stepping method. Extra torque disturbance is analyzed using fractional mathematics and a non-integer state predictor is proposed for the estimation of the state vector. For the lumped uncertainty, a fractional order compensation control is formulated using Lyapunov method. Algebraic estimator is derived to estimate the unknown parameters of the system. The proposed controller is simpler in structure and robust to noise, initial conditions. Simulation results authenticate the performance of the proposed control method.