In this paper, the definition of seaport fairway capacity, considering port service level, is given by referring to both road and inland waterway capacity combined with the features of coastal fairways. In view of the navigation environment and ships' behaviour, the safety distance of ships entering and leaving a seaport is chosen as an overall index to evaluate the navigational safety level of a fairway. Based on the ship-following theory, an Arena-based seaport operating system simulation model is constructed to analyse the impact of safety level on seaport fairway capacity. For different navigational safety levels (i.e., minimum, general and adequate), seaport fairway capacity corresponding to different service levels and navigation durations is obtained. The results show that fairway capacity varies with safety level for a given port service level, and the lower the safety level is, the higher the fairway capacity is. Finally, a recommended navigational safety level and its associated fairway capacity are given to provide a theoretical foundation for fairway design and management.