In this work, a novel distributed fault-tolerant control strategy is proposed for cooperative operation of high-speed trains (HSTs) subject to unmodeled dynamics, time-varying external disturbances, input saturation and actuator partial failures. The cooperative control of HSTs is first transformed to the consensus problem of a multi-agent system. Then, the distributed control laws that are equipped with a command filter and an adaptive neural network are developed to achieve the consensus task among the HSTs with predefined displacement and speed profiles. Further, an auxiliary dynamical system is introduced to compensate for the influence of input saturation. Moreover, an adaptive failure compensation strategy is designed to deal with the unknown and time-varying actuator faults. The convergence of the proposed controller is analyzed rigorously by applying the Lyapunov theorem, and the effectiveness is demonstrated by numerical simulations.