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Making appropriate decisions is one of the essential prerequisites for achieving desired effects in management and decision-making with any economic entity. Most of the tasks and problems in analyzing, planning and management of a port have very complex goals, with different scenarios and alternative solutions, as well as evaluation criteria and restrictions, which result in the inability of their uniform solution. In this paper, one of the processes of multi-criteria decision-making via a computer program based on the process of different scenarios ranking was used for decision-making and the development of a model of county ports system management. Also, the problem of managing the system of the county ports of Croatia was firstly considered as a whole, i.e. a system, and then its components are analyzed, followed by a synthesis, employing the multi-criteria analysis. As to acquire actual solutions and develop a new model of county ports system management, the Primorsko-goranska County is analyzed, by using the multicriteria analysis PROMETHEE procedure, with a corresponding computer program for multi-criteria decision-making. [PUBLICATION ABSTRACT]