The inverters used to drive Brushless DC motors (BLDC) include switching devices such as FETs and the faults in FETs cause severe performance degradation in systems where a BLDC acts as actuator. This paper presents a fault detection and isolation method for the FETs of an inverter for BLDC motor control systems, which is based on the EKF (Extended Kalman filter). Firstly, an equivalent circuit model for a BLDC motor plus its inverter system was derived. Secondly, a state-space equation was established, where the on-resistance of the FETs is expressed as a state variable and the EKF equation estimates the on-resistance. If the estimated resistance differs greatly from the known value, it can be asserted that there is a fault on that FET. Thirdly, the local convergence of the established EKF was proved. Finally, through the experiments, the performance of the proposed method was verified. The results show that the on-resistance is estimated close to the value specified in the FET data sheet in normal operation, whereas the estimated resistance is a much larger value than the normal one in case an FET fault occurs. Therefore, it is confirmed that the proposed fault detection and isolation method works appropriately in real systems.