In this paper, we study a disturbance observer (DOB) based controller for an EMS(Electro-Magnetic Suspension) system in presence of mass uncertainty and input disturbance. The DOB based controller is employed in order to compensate the modeling uncertainty and attenuate disturbance signals. For the design of DOB based controller, the Jacobain linearization of nonlinear system model equation is used. Computer simulation is carried out for nonlinear model in order to compare the performance of the proposed DOB controller with that of the conventional PID controller. The simulation results show that the substantial improvement in the performance can be achieved by the proposed DOB controller.