This study was aimed to investigate the influence of the linear guide configuration on the dynamic characteristics of a gantry milling machine. To predict the dynamic characteristics, we created the finite element model of the gantry machine, in which linear components were also included and modeled with the introduction of the contact stiffness defined by Hertz contact theory. Using this model, the vibration modes dominating the dynamic stiffness were determined. The results of the finite element simulations reveal that the linear guides with different preloads greatly affect the dynamic responses of the spindle tool. These results were validated by performing vibration tests on the milling machine prototype. Comparisons of the predicted results and experimental data show good agreements between them. According to the analysis results, the maximum dynamic compliance can be increased by 33% in X-axis direction and decreased by 18% in Y-axis direction, respectively when the linear guides are changed from low to high preload. Overall, current results clearly suggest that the proposed gantry model can be used to evaluate how the specification of the linear components can affect the machining performance of the milling machine.