The main challenge for container ports is the planning required for berthing container ships while docked in port. Growth of containerization is creating problems for ports and container terminals as they reach their capacity limits of various resources which increasingly leads to traffic and port congestion. Good planning and management of container terminal operations reduces waiting time for liner ships. Reducing the waiting time improves the terminal’s productivity and decreases the port difficulties. Two important keys to reducing waiting time with berth allocation are determining suitable access channel depths and increasing the number of berths which in this paper are studied and analyzed as practical solutions. Simulation based analysis is the only way to understand how various resources interact with each other and how they are affected in the berthing time of ships. We used the Enterprise Dynamics software to produce simulation models due to the complexity and nature of the problems. We further present case study for berth allocation simulation of the biggest container terminal in Iran and the optimum access channel depth and the number of berths are obtained from simulation results. The results show a significant reduction in the waiting time for container ships and can be useful for major functions in operations and development of container ship terminals.