Over the recent years, passenger flows vary frequently causing disturbances on trains operation and unsafe overcrowded environments for passengers. In congested cases, the passengers demand can exceed the available trains' capacities, implying some passengers may be left at the stations, without boarding the trains. To improve the performance of rail systems under such disturbed scenarios, this paper presents a control method to regulate disturbed passenger flows and rail system. A discrete event traffic model coupling dynamics between staying times at stations and accumulated passengers at platforms is formulated. A new method is introduced allowing real time measurements on a time based system to evaluate the discrete event state. The suggested control method applies actions both on the train traffic and stations' facilities, using a model predictive control approach. Actions at each stage are calculated as a solution of quadratic programming problem with regulation objective, and safety, feasibility, and limited trains and platform capacities constraints. Moreover, the objective function accounts passengers at platforms to reach effective flows during the controlled period. A numerical example is given to demonstrate the rail system performances under the proposed control method.