A 500Wh class high-speed Flywheel Energy Storage System (FESS) driven by a built-in BLDC motor/generator has been designed, which runs from 30000 to 60000rpm nominally. Due to the motor/generator inside, the flywheel rotor made of composites supported by PM/EM hybrid bearing system has a shape of bell or pendulum and thus requires accurate rotordynamic analysis and prediction of its dynamic behavior to secure the operating reliability. Rotordynamic analyses of the flywheel rotor-bearing system revealed that the bell shaped rotor has two conical rigid-body modes in the system operating range and the first conical mode, of which nodal point lies in the radial EM bearing position, can adversely affect the dynamic response of the rotor at the corresponding critical speed. To eliminate the possibility of wild behavior of the rotor, two guide bearings are adopted at the upper end of the rotor and motor/generator. It was also revealed that the EM bearing stiffness if 0.5~1.0E+6 N/m and damping of 2000 Ns/m are favirable for smooth operation of the system around the 2nd critical speed.