This study develops methods for countering schedule disruptions in intermodal or intramodal freight transportation systems operating in time-dependent, stochastic, and dynamic environments. When routine disruptions occur (e.g., traffic congestion, vehicle failures, or demand fluctuations) in preplanned intermodal timed-transfer systems, this dispatching control model determines through an optimization process whether each ready outbound vehicle should be dispatched immediately or held waiting for some late-incoming vehicles with connecting freight. Another submodel is developed to deal with the freight left over because of missed connections. Through a series of cases solved with a hybrid genetic algorithm–sequential quadratic programming algorithm, the model demonstrates its ability to minimize net costs through its dispatching decisions.