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Transportation infrastructures, particularly those supporting intermodal freight, are vulnerable to natural disasters and man-made disasters that could lead to severe service disruptions. These disruptions can drastically degrade the capacity of a transportation mode and consequently have adverse impacts on intermodal freight transport and freight supply chain. To address service disruption, this paper develops a model to reliably route freight in a road-rail intermodal network. Specifically, the model seeks to provide the optimal route via road segments (highway links), rail segments (rail lines), and intermodal terminals for freight when the network is subject to capacity uncertainties. To ensure reliability, the model plans for reduced network link, node, and intermodal terminal capacity. A major contribution of this work is that a framework is provided to allow decision makers to determine the amount of capacity reduction to consider in planning routes to obtain a user-specified reliability level. The proposed methodology is demonstrated using a real-world intermodal network in the Gulf Coast, Southeastern, and Mid-Atlantic regions of the United States. It is found that the total system cost increases with the level of capacity uncertainty and with increased confidence levels for disruptions at links, nodes, and intermodal terminals.