Structures constructed on soft soils may undergo significant settlement, local or global instability, and a significant lateral displacement of the soft soil layer. Ordinary stone columns (OSC) and stone columns strengthened with geosynthetic reinforcement reduce settlement and improve the subsoil's bearing capacity. Numerical analyses have been performed using a 3-dimensional finite element program (PLAXIS3D) to investigate the time-dependent behavior of embankments resting on stone columns constructed in very soft clay. The geosynthetic encasement is the more typical type of reinforcement; however, laminated layers can be adopted in this study. The geosynthetics material was used to strengthen the OSC in the form of vertical encasement, horizontal stripes, and combined vertical-horizontal reinforcement and vertical-basal geogrid reinforcement (BGR). This research compares these forms of reinforcement on embankment behavior. The research results showed that using the encased stone column (ESC) and the vertical-horizontal reinforced stone columns (V-HRSC) have provided a considerable improvement in the lateral deformation of the column over its length, generation, and dissipation of excess pore pressure, and settlement. An increase in factor of safety (FOS) against failure of the embankment was observed by 53% using the ESC compared to untreated soil. Using the horizontal geosynthetic layer (HGL) and the (BGR) after encasing the stone columns has no effect on the safety factor as the failure mechanism converted from deep-seated to surface failure.