It is clearly understood that e-navigation is beneficial to prevent collision and grounding of ships. The purpose of this study is to define and present a future ship operation system under the e-navigation environment in order to provide clear direction for the design of Korean e-navigation system. The future ship operation system consists of shipboard navigational system, shore supporting system and maritime communication system. To achieve the objectives of this study, the ship operation system was discussed separately into SOLAS ships and non-SOLAS ships in this study. In SOLAS ships, mariners become a system manager, choosing system presets, interpreting system output, and monitoring vessel response. In small ships and fishing vessels, mariners may enjoy their navigation by using the automatic tracking of ship’s position on the portable electronic chart display. The improved bridge design, integrated and harmonized navigational system and single window reporting will reduce significantly the administrative and physical workload of mariners. Mariners can concentrate their attention more on navigational duty under the e-navigation environment. To build an effective Korean e-navigation system, the essential navigational functions and e-navigation services for small ships and fishing vessels must be identified and developed taking into account user needs.