This paper is concerned with the computer-based sliding mode control of flexible rotormagnetic bearing systems (FR-MBS). The plant dynamics consisting of actuator dynamics and flexible rotor dynamics are described. The reduced-order model for controller design is given by eliminating higher-order modes of the mechanical and electrical magnetic interaction system. A discrete-time sliding mode controller with a new robust reduced-order variable structure system (VSS) observer is proposed and its robust performance is evaluated with several simulations based on a calculation model. This digital controller is implemented to replace a linear analogue PID compensator. Levitation tests using the proposed digital controller are performed and compared with those of the PID compensator. The unstable modes can be easily controlled with the good stability and the spillover phenomena due to ignored higher-order modes are not generated. It is indicated that the discrete-time sliding mode control has robustness to the model parameter variations and external disturbances. Using the discrete time sliding mode controller with the reduced-order VSS observer, the test rig of the magnetic bearing system can be successfully rotated in a speed range of 0-35000 rpm, which includes the first critical shaft frequency of the flexible rotor.