Magnetic levitation systems are widely used in various industries. These kind of systems are usually open-loop unstable and are described by highly nonlinear differential equations which present additional difficulties in controlling these systems in the presence of disturbance and sensor noise. We consider the stabilization and the tracking problems of a magnetic levitation system. In this paper an adaptive fractional order Backstepping sliding mode control schemes is proposed. Backstepping algorithm is based on the Lyapunov theory. The proposed controller in this paper is designed by a combination of a Backstepping algorithm, sliding mode control and fractional calculus to make more degree of freedom and robustness. The stability of the closed loop system is investigated by using the Lyapunov stability theorem and the new extension of Lyapunov stability theorem for fractional order systems. Simulations are performed to confirm the theoretical results of the proposed controller for the magnetic levitation system. The proposed controller is able to reject the sensor noise and disturbance with a chattering free control law. Finally the simulation results of the proposed controller are compared with the adaptive fast terminal sliding mode control.