In this paper a 3D numerical model using a software based on the Finite Element Method (FEM), was developed and validated using the results obtained in a geotechnical centrifuge model of a piled raft system founded in soft soils undergoing regional subsidence. The piled raft configuration had nine piles distributed in the center of the raft. The kaolin parameters were obtained, calibrated, and validated for the Hardening Soil Model (HSM), based on laboratory triaxial and oedometer test results. Also, a single pile load test was carried out in the centrifuge to get the resistance parameters used in the FEM. The developed numerical model reproduced satisfactorily soil and foundation consolidation displacements due, not only by the structural service load but also by the pore pressure drawdown. For load distribution on piles and raft, the model reproduces with good agreement the foundation behavior only for the structural service load, for pore pressure drawdown some adjustments on the embedded piles elements shaft and base resistance had to be done. The developed model allowed to identify the most sensitive parameters for this type of simulation, to define the types and stages of analysis that had the best fit for the physical model, and to obtain additional results to those measured in the physical model, e.g., the axial load distribution developed along the piles and therefore the magnitude of the negative skin friction, that is an important load that should be considered for the structural safety review of piled foundations subjected to this complex conditions.