When we design a controller for the active magnetic bearings that support a large rotor, it is important to have an accurate model of the rotor. For the case of the flywheel that is used to store energy, an accurate rotor model is especially important because the dynamics change with respect to the running speed due to gyroscopic effects. In this paper, we present a procedure of obtaining an accurate rotor model of a large flywheel energy storage system using finite-element method. The model can predict the first and the second bending mode which match well with the experimental results obtained from a prototype flywheel energy storage system.