Automatic operation of high speed trains (HSTs) requires dedicated control schemes to tackle uncertain dynamics, unknown resistive forces, coupling nonlinearities, interactive in-train forces, unexpected disturbances, and faults. This paper addresses the problem of position and velocity tracking control of HSTs with multiple vehicles connected through elastic couplers. A neuro-adaptive fault tolerant control scheme is developed to compensate the input nonlinearities due to traction or braking notches, uncertain impacts from in-train forces, resistive aerodynamic drag forces, traction or braking faults, and adherence-antiskid constraints. High precision velocity and position tracking is achieved by using the proposed control scheme that combines the robust adaptive control with nonlinearly layered neural networks. Closed-loop stability is ensured with strict mathematical analysis. The effectiveness of the proposed approach is also validated through numerical simulations with considering the adherence-antiskid constraints.