In this paper, we present a two-stage mixed integer programming (MIP) interdiction model in which an interdictor chooses a limited amount of elements to attack first on a given network, and then an operator dispatches trains through the residual network. Our MIP model explicitly incorporates discrete unit flows of trains on the rail network with time-variant capacities. A real coal rail transportation network is used in order to generate scenarios to provide tactical and operational level vulnerability assessment analysis including rerouting decisions, travel and delay costs analysis, and the frequency of interdictions of facilities for the dynamic rail system.