This paper presents a finite element investigation into the copper losses and rotor eddy current losses in brushless DC motors used in a flywheel energy storage system. The copper and rotor losses generate heat which needs to be dissipated in order to not exceed a defined temperature level for the magnet or winding insulation to avoid demagnetization or damage, which if it occurs will reduce the motor performance. The principle of operation and losses calculations are presented in the paper. The influences on the copper and eddy current losses are analyzed in detail, including the operation mode, the control strategy and the variation of the speed. Simulation and experimental results are presented and discussed.