City competitiveness is a complex product of local and international conditions, local characteristics, social and economic superstructure, and the actions of individual companies. Although many scientific studies have examined the country’s and urban competitiveness, the competitiveness of port cities still needs to be assessed comprehensively, taking into account their crucial economic role. The purpose of this paper is to evaluate the competitiveness and economic security of the Baltic port cities (Klaipėda, Riga, and Tallinn). Statistical processing and multi-criteria evaluation methods (SAW, COPRAS, and TOPSIS) were chosen to achieve this goal. The comparative analysis showed that the population change in port cities is not significant for the final result of the competitiveness assessment, and the unemployment rate in port cities is lower than in the country. The assessment of the competitiveness of port cities from the point of view of economic security shows (after checking such indicators as unemployment rate, company income, and infrastructure) that Tallinn is the most competitive port city according to the three multi-criteria evaluation methods, while Klaipėda is the least competitive. The assessment was carried out in three stages to monitor changes in the situation of port cities, compared to changes in a certain indicator and the costs of timely solutions or the improvement of the city’s position in relation to other cities.