Automation ensures accurate and well-organized container transportation in container terminals. This paper addresses operational issues such as equipment scheduling and the coordination between various pieces of equipment in a rail-based automated container terminal. Containers are relayed using multiple types of equipment from road trucks to a vessel and vice versa. Therefore, handshaking is required during a container transfer between different pieces of equipment. Synchronization between the schedules of all the equipment is important to reduce equipment waiting times and the time required for transporting containers, which results in a short turnaround time for a vessel. This paper proposes an integrated control system with the objective of synchronizing the operations of different types of equipment, provides a list of decisions to be made by the control module of each type of equipment, and shows all the required information transfers between control modules. A scheme for the integrated scheduling of multiple types of equipment is proposed. The decisions made by each control module in a real-time fashion are listed with detailed explanations, and the information transfer between managers in a real-time situation at the proposed terminal is described.