Nowadays, some projects have to be constructed in areas having thick layers of soft clay. These soft soils with low shear strength and high voids ratio, lead to excessive settlements even if subjected to low vertical or lateral loads. For this reason, soft clays are considered problematic soils for foundation purposes. Several improvement techniques have been done to enhance such clay. Stone columns have been used to improve soft soils by increasing it carrying capacity and reducing the settlement. In this paper, a numerical study on seismic behavior of stone column in soft clay subjected to earthquake loading has been performed. A two-dimensional plane strain program PLAXIS (dynamic version) is used for the present numerical modeling. A series of modeled stone columns were simulated with different diameters and spacing between columns. Also, the influence of geotextile encasement on the performance of stone columns, foundation systems in soft clay is investigated and compared with the behavior of ordinary stone columns without casing. The results showed that the ordinary stone column with small spacing and larger diameter has a greater bearing capacity and give a smaller settlement, compared to the column with large spacing. In addition, the geotextile encasement for stone column can be provided a significant increase in stone column capacity as well as a huge reduction in settlement is considered with increasing the encasement strength.