In many parts of northeast India, in order to achieve a sustainable infrastructure based on minimal distance and gradient criteria, railway tracks often have to pass through a marshy deposit with significantly poor bearing capacity. Consequently, the laid tracks undergo significant long-term settlements due to creep-induced dissipation of excess pore pressure from the underlying low-permeable soft cohesive deposits, thereby necessitating ground improvement. Among several techniques, a sustainable one has to be decided to ensure long-term unhindered functionality of the adopted methodology. In lieu to this understanding, a case study of the Udaipur railway embankment in Tripura, India, is presented. The embankment, raised over a thick bed of soft soil, suffered extraordinary settlement. Consequently, prefabricated vertical drains (PVDs) were used as a method of ground improvement. In this regard, a plane strain finite element (FE) analysis is carried out for predicting the consolidation settlement due to the staged loading of the embankment and the evolution of excess pore pressure dissipation from the layered substratum improved with PVDs. Mohr–Coulomb (MC) constitutive model is used for representing the embankment and cohesionless layers, while the soft cohesive soils are represented using Soft Soil model. The PVDs are simulated as ideal drains by employing 1D “drain” elements. In contrary to the conventional approach of considering layered horizontal substratum, the importance of considering the realistic undulated substratum is highlighted. It is exhibited that design based on the conventional approach might be insufficient in draining out the pore water in case a basin is formed in an undulating low-permeable layer beneath the designed length of the PVD, thereby elucidating the sustainability in the considered approach.