The load deformation of ballasted rail tracks subjected to cyclic loading is investigated experimentally using a large-scale track process simulation apparatus and numerically through a combined discrete element–finite-difference approach. Laboratory tests were performed to examine the deformation and degradation of ballast subjected to cyclic loading at 15 Hz and a lateral confinement of 10 kPa 10 kPa. The laboratory results reveal that ballast undergoes significant deformation during the initial load cycles, followed by gradually increasing deformation attaining a steady value toward the end of testing. A numerical model based on a combined discrete element method (DEM) and finite-difference method (FDM) is introduced to study the load-deformation response of the ballast assembly while considering interaction between the ballast aggregates and the subgrade layer. In this coupled model, the discrete ballast grains are modeled by DEM, and the subgrade domain is modeled as a continuum by FDM. Interface elements are introduced to transmit the interacting forces and displacements between adjoining material domains in which the DEM transfers contact forces to the FDM, and then the FDM updates the displacements, which provides subsequent input into the DEM. This computational cycle continues with the increasing number of loading cycles. The numerical model is validated by comparing the predicted cyclic load-deformation response with the laboratory measurements. Contact force distributions and stress contours in the assembly are analyzed and presented graphically to interpret the behavior of the model track, and the effects that subgrade stiffness have on the axial strain and bond breakage of the ballast are investigated. This combined DEM-FDM analysis is also used to analyze the load deformation of an instrumented track in the town of Singleton, Australia, and the numerical predictions are compared with the field data.