This contribution investigates the economic benefits of using weather ship routing on Short Sea Shipping (SSS) activities. The investigation is supported with the development of a ship routing system based on pathfinding algorithm, the parametrization of the wave effect on navigation, and the use of high-resolution meteo-oceanographic predictions. The optimal ship routing analysis is investigated in a European SSS system: the link between Spanish and Italian ports. The results show the economic benefits using ship routing in SSS during energetic wave episodes. The rate of cost savings may reach 18% of the total costs under particular bad weather conditions in the navigation area. The work establishes the basis of further developments in optimal route applied in relatively short distances and its systematic use in the SSS maritime industry.