EOTS(Electro-Optical Tracking System) provides stabilized images while tracking a moving target. EOTS consists of a variety control circuits, sensors, and drive parts. The failure of EOTS may give a significant impact on expensive internal equipments and aircraft. Therefore, EOTS should be checked for faults before operation and during operation. This paper presents a fault detection and isolation method for EOTS actuation part. while the fault detection being done in real time. Once a component fault is detected, EOTS will automatically stop and the fault isolation follows. Actual equipment tests conforms the validity of our scheme.