In this study, two analytical fractional order controller design methods are applied to magnetic levitation experiment set. The design methods are known as "Set-Point Weighted Fractional Order PID" and "Filtered Fractional Order PI" controller design methods. In order to be able to apply these design methods, magnetic levitation system is stabilized using a PID controller. Then, fractional and integer order models of the stabilized system are identified. The fractional operator is approximated using Oustaloup filter approximation. In both design methods the controllers are expressed using the parameters of the closed-loop transfer function that are determined by the designer. The effects of the variation of the design parameters on system performances are examined on real time application. Moreover, the design parameters are optimally selected according to a performance index and then they are applied to the stabilized system. Furthermore, the disturbance rejection and noise reduction performances of the controllers are compared with each other.