Geosynthetic can be used as an encasement for conventional stone column, forming geosynthetic encased stone column (GESC). This method can reduce the lateral displacements of stone column and improve the bearing capacity in soft clay through the radial restraint of geosynthetic encasement. This paper presents a numerical study to investigate the dynamic response of GESC in soft clay foundation. Both the stone column and the soft clay were characterized using nonlinear elasto-plastic models that consider the hysteretic behavior. Geosynthetic encasement was characterized using linearly elastic geogrid elements. The 3D dynamic numerical model was validated using shaking table test results published. A parametric study was conducted to investigate the influences of geosynthetic encasement stiffness, soft clay shear modulus, and embankment loading on the dynamic response of GESC in soft clay foundation. The results show that with the increase of geosynthetic encasement stiffness and soft soil shear modulus, the decrease of embankment load, the settlement of stone column and the strains of geosynthetic encasement and soils could be significantly reduced. Geosynthetic encasement could effectively improve the seismic performance of stone column in soft clay foundation.