The dynamic facility layout problem considers flow over multiple time periods in an environment where the material flow between departments changes over time. If this complex problem is combined with the other system problems, such as material handling system designing, this results in a more complicated problem. In most recently proposed approaches for these two synchronized problems, the integrated formulations have been used where the objective function is a weighted sum of some conflicting objectives that may belong to either one or different decision makers. In the former case, the poor practicability of such an approach is due to the difficulty of normalizing these functions and of quantifying the weights. In addition to these problems, in multiagent systems with a strong cooperation, there is another important problem in incorporating the conflicting objectives of conflicting decision makers that is not considered in the existing researches. By these descriptions, developing some other solution strategies, such as iterative or hierarchical methods, are necessary for these cases. In this paper, a bilevel model is developed. The experimental results reveal significant enhancements with respect to more classical approaches (i.e., integrated formulation and Pareto optimal solutions) based on the proposed bilevel model and algorithms.