This paper proposes an algorithm called multi-objective optimization using differential evolution (MOODE) for providing the optimal mathematical model of flexible beam system. The main reason of developing a flexible beam system is to find an appropriate controller to control the vibration produced by this system. This dynamic system is treated as a black box where the acquired input-output data is used in the modeling processes. Two objective functions are considered for optimization; minimizing the number of term of a model structure and minimizing the mean square error between actual and predicted outputs. Nonlinear auto-regressive with exogenous input (NARX) model is used to represent the mathematical model of the investigated system. To obtain an optimal model for representing the dynamic behavior of flexible beam system, the model validity tests have been applied.