This paper introduces the modeling and an improved controller design for a driving system for a DC Flywheel Energy Storage System (FESS). The Driving system is based on a Bi-directional Buck-Boost converter, the accurate modeling of the system including the parasitic resistances for all the components is carried out. In this model, the equivalent circuit of the machine is integrated in the converter state space model for improved accuracy and controllability. The system has two operating modes; when the machine is charging, the converter is operated in the buck mode. A controller is designed to regulate the charging rate through controlling the machine terminal voltage. In the discharging mode, the converter is operating in the boost mode, a current controller is taking over to control the injected current from the machine to the DC bus. The detailed design of both control loops is explained. Simulation results show the accuracy of the derived model and the enhanced performance of the FESS. Further, it is shown that the reversal of power flow direction is done seamlessly.