In this paper agent-based model of migration flows to European Union countries that is taken into account individual preferences of agent-migrants is presented.The model is implemented in the AnyLogic system.Such model is based on using systemdynamics and agent-based modelling methods which applying allowed taking into account individual decision-making system of agent-migrants.Such system allows forecasting the dynamics and structure of migration flows to European Union countries with the influence of fundamental macroeconomic characteristics of European countries (e.g.GDP, manpower costs, the level of social expenses, etc.), as well as characteristics of agent-migrants (e.g. the homeland country, age, social status, etc.) that impact on the individual decision-making system.