This paper is about an advanced braking control strategy for rail transportation systems. The motivation is to improve the efficiency of the control in real-world conditions taking into account modeling errors, unknown perturbations and occurring failures. This will allow traffic frequency improvement along with overall safety and security enhancement. The strategy is based on an integrated approach, including a fault tolerant control strategy along with perturbation estimation and compensation, and a fault detection module. Fault detection, if positive, will be used to switch the controller into a “safe mode” avoiding the fault and improving control precision with respect to stopping position requirements. Simulations are provided to prove the efficiency of the proposed approach.