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Greece has seen a great inflow of refugees the past the past three years. They are coming from countries torn by persecutions, wars and dire economic conditions. These refugees choose Greece due to its strategic position as an entry point to more developed countries in Europe. However, due to a combination of reasons, they can be forced to remain in Greece for an extended period. Taking also into account that a percentage of the refugee flows is children, it increases the need to provide a just an equal education to these children. The objective of the present thesis is to answer the question of how refugee flows can affect the system of primary education in Greece. To achieve the objective, two methods were employed. First, an extensive literature review on the issue of primary education and refugees. The review is divided into two parts: the first is focused on the system of primary education itself, while the second deals with the psychological aspects of refugee children during their transition to a new system of education. The literature review is used as a basis for the development of a quantitative Causal Loop Diagram (CLD) with the method of System Dynamics. Major notions are translated as systemic variables and their major causal relations are identified. The analysis of the diagram reveals that training programs targeted at school teachers and cooperative actions targeted at students and parents (refugees and local) can determine the success of any central policy regarding the integration of refugees in primary education. Finally, the stance of (local) school leadership is of the utmost importance, as it can ease the integration of refugee children an at the same time mitigate any xenophobic reactions from the local population.