The utilization of rubber-coated ballast (RCB) aims to enhance the energy dissipation capacity and decrease the rate of deterioration of ballasted tracks, leading to reduced maintenance costs. Ballast fouling can affect the ballast's drainage properties, shear strength, deformation, and resilience that may ultimately lead to track misalignment. In this context, in the present study, the drainage and shear characteristics of RCB and RCB-conventional ballast mix are evaluated for various levels of clay fouling. The results of permeability tests indicated that the hydraulic conductivity (k) of RCB is more than that of conventional ballast. For example, the k of RCB is 71% higher than that of conventional ballast (fouling content = 50%). However, the k of ballast decreased significantly with the increase in the content of clay fouling. The results from the direct shear tests revealed that both RCB and RCB50% perform poorly in terms of peak friction angle (φ) when compared to conventional ballast. With the addition of clay fines, a further reduction in the shear strength is observed. For instance, the φ of unreinforced RCB, RCB50%, and conventional ballast decreases by 18.5%, 14.2%, and 10.4%, respectively, with the increase in fouling content from 0% to 50%. However, in case of geogrid-reinforced RCB50%, the peak friction and dilation angles are found to be relatively higher as compared to unreinforced conventional ballast in both clean and fouled conditions. The results of cyclic tests demonstrated that the deformation of both unreinforced and geogrid-reinforced RCB-conventional ballast samples increased while the resilience modulus (Mr), damping ratio (Dr), and ballast breakage index (BBI) decreased with the increase in fouling content. Moreover, the inclusion of geogrid significantly reduced the extent of deformation and particle breakage but enhanced the Mr and Dr when compared to unreinforced ballast. The various test results suggest that the geogrid-reinforced RCB50% performs better than unreinforced conventional ballast under both clean and clay fouling conditions. For geogrid-reinforced RCB50%, the volumetric strain (εv) and BBI are reduced by 9.7% and 69.5%, while Mr and Dr are improved by 5.75% and 176.5% as compared to unreinforced conventional ballast (fouling content = 20%). Additionally, empirical relations are developed to predict the vertical strain (ε1), lateral strain (ε3), Mr, Dr, and BBI of RCB-conventional ballast mix under clean and clay-fouled conditions.