This paper presents an application of Model Reference Adaptive Control (MRAC) method based on MIT rule for closed loop fractional-order control systems. The main advantage of the method is that it may gain adaptation capability for existing fractional-order systems. It essentially contains two loops, which are the inner loop for fractional-order PID ( FOPID) control of plant, and the outer loop for implementation of MIT rule for model reference adaptive control. This approach do not modify any parameter of existing closed loop control system, instead it performs input shaping for the closed loop control system so that response of closed loop control system approximates to a desired control response, which is described by the reference model. The method can be useful in fault diagnosis and fault-tolerant control of systems because it may allow maintaining control performance for tolerable system perturbation. The paper presents a simulation study for FOPID and plant models that were obtained by Fractional-order Modeling and Control (FOMCON) toolbox. Results showing the response of proposed system for amplifications type faults are also discussed.