In this study, rainfall infiltration in vault of the second near-surface disposal facility was evaluated on the basis of various disposal scenarios. A total of four different disposal scenarios were examined based on the locations of the radioactive waste containers. A numerical model was developed using the FEFLOW software and finite element method to simulate the behavior of infiltrated water in each disposal scenario. The effects of the disposal scenarios on the infiltrated water were evaluated by estimating the flux of the infiltrated water at the vault interfaces. For 300 years, the flux of infiltrated water flowing into the vault was estimated to be 1 mm/year or less for all scenario. The overall results suggest that when the engineered barriers are intact, the flux of infiltrated water cannot generate a sufficient pressure head to penetrate the vault. In addition, it is confirmed that the disposal scenarios have insignificant effects on the infiltrated water flowing into the vault.