Prefabricated vertical drains made from natural materials such as jute and coir are fast emerging as a practical alternative to synthetic drains because they have excellent engineering properties and they are biodegradable and environment friendly. While previous studies indicate that the biodegradation of drains can sometimes be exacerbated when they are exposed to adverse environmental conditions, thus making the dissipation of excess pore pressure considerably retarded, those which use numerical modelling to incorporate the implications on soil consolidation are limited. This study therefore aims to carry out a numerical investigation based on the Finite Element Method (FEM) to evaluate how biodegradation affects consolidation via a subroutine which can capture the reduction in drain permeability over time and incorporate it into the FEM. Unlike conventional methods which do not consider the drain degradation, the results of this study reveal that the dissipation of excess pore pressure can be retarded when a drain decays rapidly. Subjected to different degradation characteristics such as the degradation with and without an initial intact period, soil consolidates at different rates although the discharge capacity in those cases decreases to the same final value. The numerical solution is also applied to model a laboratory study, and the result shows a certain agreement with experimental data, indicating that FEM with support from the subroutine can capture the influence of drain degradation on soil consolidation well.