This study presents an optimized system for ship route planning. Computational fluid dynamics simulations were used to modify Kwon’s semi-empirical speed loss estimation method, enabling efficient route planning under variable sea conditions. The study focused on improving the prediction of speed loss in irregular waves for container ships and further applying this to ship-optimized voyage planning. Dynamic programming was used for optimized voyage planning by modifying the ship course in response to meteorological data; this approach could balance both energy efficiency and safety. The modified speed loss predictions aligned closely with the simulation results, enhancing the reliability of weather routing decisions. Case studies for trans-Pacific and trans-Atlantic voyages demonstrated that the proposed system could significantly reduce the voyage time. These findings highlight the potential of real-time updates in voyage planning. The proposed system is a valuable tool for captains and fleet managers. The applicability of this system can be further broadened by validating it on different ship types.