Excessive settlement due to consolidation can cause damage to the structure’s rest on soft soil. The settlement takes place in relatively longer. The preloading and prefabricated vertical drain (PVD) is often applied to accelerate the primary settlement. The issue in this research is the estimation of the settlement. The Asaoka method and the finite element method using PLAXIS-2D are used to estimate the final settlement of a PVD treated embankment. For the former, a complete record of the settlement was required; for the latter, some ground parameters are needed for the PLAXIS-2D analysis, such as the permeability of the soil. Because the installation process of PVD tends to influence the permeability of the in-situ soil around the PVD, the soil permeability after the installation of PVD needs to be adjusted. The numerical results were compared with actual settlement data to find out the best-fit input parameters (i.e. soil permeability) of the actual data. It was found that the best-fit soil permeability (k) used in the numerical study was about one-half of the k value determined from the laboratory test. The Root Mean Square Deviation shows that the settlement predicted by the numerical analysis has approximately 30% of the actual settlement.