We develop an aerodynamic loading assignment model for intermodal freight trains based on an integer-programming framework to help terminal managers make up more fuel-efficient trains. This is the first use of optimization modeling to address the aerodynamics and energy efficiency of railroad intermodal trains. Several recommendations regarding railway equipment use, operations, and policy are proposed to improve fuel-efficiency and reduce emissions from intermodal transportation. Analysis of one major railroad intermodal route reveals the potential to reduce fuel consumption by 15 million gallons per year with corresponding savings of $28,000,000. Greater benefits are possible through broader implementation of the model.