Materials, products and workers have to move in order to perform the daily schedule of the organizations. This movement which is done by vehicles or material handling systems is an important cost element for the organizations. A good facility layout design may reduce this cost by minimizing the interdepartmental flow. Till today, most of the facility layout planning studies have been focused on production facilities. On the other hand, having vehicles with high fuel consumption and having continuously moving personnel makes facility layout important for also military facilities. In this study, in order to remedy this deficiency in the literature, we focused on military facilities. In addition to conventional transportation costs, the allocation of infirmary and quick reaction team which affects human health and personnel safety has also considered. We presented a multi-objective mixed integer programming model for this bi-objective facility layout problem. We applied this model on a military facility problem which is created by utilizing real data.