Multiple or split N fertilizer applications during a single cropping period is a recommended practice for controlling N (specifically NO3–N) leaching into groundwater. Here, we demonstrate the benefit of split fertilizer applications in two typical upland soils of Japan (sand and Andosol) using a combination of a laboratory experiment and modeling. Soil water flow and N transport properties of the soils were measured using standard procedures. Transient N and water transport experiments were conducted in cylindrical soil columns under single (lumped) and split NH4–N applications. The column experiments were successfully simulated using Richards' equation and an advection–dispersion model with equilibrium nonlinear sorption conditions and first-order transformation for N speciation. Using the model for the two soils, several irrigation and fertilizer management scenarios were then simulated based on 1992 through 2000 meteorological data to investigate the long-term effects of lumped and split fertilization schedules for a representative set of crop and irrigation conditions. In comparison with lumped applications, split fertilizer applications were found to consistently reduce the amount of N leaching, even though year-to-year differences of N leaching reductions between sand and Andosol were significant. For unstressed crops, the actual reduction in N leaching are shown to depend on the timing of precipitation and irrigation events, on soil type, and on plant N uptake behavior. However, across all scenarios, two split applications instead of a single, lumped application reduced the N leaching fraction by approximately one-third. In the sandy soil, a three-way split resulted in further leaching reductions compared with the two-way split. Six-way split applications did not result in further N leaching improvements in either sand or Andosol. After adjusting N application rates to account for reduced N use efficiency, N leaching rates for unstressed crops under lumped fertilization were found to be several times higher than under split applications.