The stability of flywheels in an energy storage system supported by active magnetic bearings (AMBs) is studied in this paper. We designed and built two flywheel energy storage systems (FESS) that can store up to 5 kWh of usable energy at a maximum speed of 18,000 rpm. One is optimized to store as much energy as possible, resulting in a flywheel with a strong gyroscopic coupling. The other has a much smaller gyroscopic coupling for ease of control. To analyze the stability of the system accurately, we derived the dynamic models of the rotor using finite-element method and integrated them with the models of the bearings, amplifiers, and sensors to obtain the simulation model of the system. We validated the model through experiments and compared the stability of these two systems.