Although magnetic bearings are generally reliable, an important concern for machine applications is fault tolerance. The fault-tolerant operation of a magnetic bearing system can be realized through the identification and isolation of fault actuators and subsequent support reconstruction via residual actuators. In this study, a novel fault-diagnosis algorithm for electromagnetic actuators (EMAs) is proposed. The equivalent slope of the load current is defined as a fault-diagnosis threshold by theoretically analyzing the variation characteristics of the current in the modulation. The synchronous sampling of the current and its processing algorithm are designed. By combining these algorithms with the generalized bias current linearization theory reported previously, a fault-tolerant control (FTC) system for magnetic bearings is developed, and control of multi-position and multi-current loops is realized by using two digital signal processors (DSP). The FTC of the rotor motion and the fault-diagnosis of actuators are executed in parallel. The proposed control system is verified by the experiments, and experimental results demonstrate that the proposed system can cope with EMA fault in an extremely short time of less than 5 ms. Thus, the support can be reconstructed by employing the FTC to maintain rotor stability.