An intermodal terminal control system determines characteristics of cargo containers scheduled for receipt into and/or travel out of an intermodal terminal connected with both rail routes and automobile routes, determines characteristics of cargo handling equipment within the intermodal terminal, determines characteristics of rail vehicles scheduled for one or more of entry into or travel out of the intermodal terminal, and determines characteristics of automobile vehicles scheduled for entry into or travel out of the intermodal terminal. The system also determines constraints on cargo handling operations and a plan for the cargo handling equipment to transfer the cargo containers between the different modes of transportation within the intermodal terminal. The plan designates a sequence of operations to be performed in moving the cargo containers with the cargo handling equipment. The plan is based on the characteristics of the cargo containers, the cargo handling equipment, the rail vehicles, and the automobile vehicles.