The PEMS high speed maglev train, which features a permanent magnet inside an electromagnet, is a new kind of maglev train for long distance intercity transportation. The joint structure, which consists of two single levitation sub‐systems, is the fundamental levitation unit. Two kinds of faults are considered and corresponding fault tolerant control strategies are proposed. The first fault condition is when a gap sensor that is part of a single levitation system is faulty. For this kind of fault, a fault tolerant control strategy based on signal reconfiguration is proposed. The second fault condition is when the whole of a single levitation sub‐system is faulty. Under this condition, a faulty model is firstly established, then a fault tolerant control strategy is designed. When this kind of fault is detected, a switch from the normal controller to the fault tolerant controller can make the faulty system stable.