This paper presents a simulation framework for the logistics operations at Smart Yards. A Smart Yard is a digital and physical system enabling the collaboration of various companies at a logistics hub, e.g., seaport, airport or hinterland distribution center, and characterized by a decoupling point, automated vehicles for internal handling of cargo, and data sharing technologies. The framework is a high-level conceptual model for a hybrid Discrete Event and Agent-Based Simulation, comprising inputs, outputs, assumptions, flowcharts, and agents representing the complex interrelation of stakeholders and shared autonomous vehicles. We illustrate the concept of Smart Yard using three case studies and apply our simulation framework to one of these cases by analyzing the use of a Smart Yard at Amsterdam Airport Schiphol.