The present study investigates subgrade response of an embankment subjected to staged train loading and rainfall using finite-element modelling approach. The mechanical behavior of the gravel layers of embankment and the in-situ soil layers were modelled using Mohr-Coulomb constitutive model while that of subgrade layers was modelled using Hardening soil with small strain stiffness model. The hydraulic behavior of the formation layers was incorporated using van Genuchten model. A fully-coupled flow deformation analysis based on Biot’s theory of consolidation was carried out to validate the developed model using field measured values of suction reported for a South-African railway track. This was followed by the staged application of pseudo-static train loading and constant rainfall using plastic and fully-coupled flow deformation scheme of analysis respectively. In addition, the subgrade response under staged loading was also evaluated through parametric study considering rainfall intensities of 20, 40, and 60 mm/day. The results indicated a gradual decrease in suction with progression of loading stages causing strain accumulation in the subgrade layer. Vertical strain in subgrade was found to increase during train loading and decrease during rainfall stages. The analysis also showed that the influence of rainfall intensity on subgrade response is governed by changes in its suction stress value with progression of loading stages. The outcome of this study contributes to a better understanding of the deformation mechanism of subgrade layer of railway embankments under the influence of train movement and rainfall conditions.