Rockfall triggered by earthquakes can cause severe infrastructure losses and even fatalities. The flexible protective barrier is an efficient rockfall protection system that has been widely used against rockfall. This studyproposed a novel approach to simulate a field test of rockfall impacting the flexible barrier, and the simulation results showed an excellent match with the field test results. Based on this approach, the seismic loading was applied to the numerical model, and four types of seismic loading were adopted, e.g., non-seismic, x-directional seismic, y-directional seismic, and z-directional seismic. This study aims at investigating the dynamic behavior of the flexible protective barrier under different seismic loading during the rockfall impact process. The following findings can be obtained from the simulation results. First of all, the seismic loading can increase the maximum elongation and decrease the final elongation of the flexible protective barrier comparing to non-seismic loading. Second, the largest deformation area of the protective barrier is at the diagonal position when x-directional seismic loading was applied, which is at the vertical bisector position when y-directional and z-directional seismic loading was applied. Third, the maximum elongation of the protective barrier decreased with the increasing seismic wave period. But in general, the amplitude and period of seismic waves have negligible effects on the elongation, maximum normal stress, and maximum shear stress of the flexible protective barrier.