Analysis of structures which are composed of numerous repeated unit structures can be simplified by using homogenized properties. If the unit structure is repeated in one direction, the whole structure may be regarded as a beam. Once the effective stiffness is obtained from the analysis of the unit structure in a proper way, the effort for the detail modeling of the global structure is not required, and the real structure can be replaced simply with a beam. This study proposes a kinematical periodicity constraint to be imposed on the FE model of the unit structure, which improves the accuracy of the effective stiffness. The method is employed to a one dimensionally arrayed 3D structure containing periodically repeated un-symmetric holes. It is demonstrated that the deformation behavior of the homogenized beam agrees well with that of the real structure.