Soft soil suffers from problems like excessive settlement or bearing capacity failure. One of the methods for improving the ground with soft clay involves utilization of stone columns. The efficiency can be improved further by providing a geosynthetic encasement to the column. The inclusion of encasing provides a separating medium between the stone column and surrounding soft soil, thus maintaining its structural integrity and confinement. This study involves a numerical analysis of the settlement behavior of the geosynthetic encased stone columns upon varying the spacing to diameter ratio and its effect on other parameters. It also investigates the settlement behavior in case of a variable spacing of stone columns along its transverse section and its comparison with other cases. The study was carried in finite element-based software Plaxis 3D using Mohr–Coulomb and modified cam clay constitutive models. The result from published literature has been considered for validation. The optimal mesh size for numerical investigation was determined through mesh convergence study. The results show that upon varying the spacing to diameter ratio of encased stone columns along the transverse section of the embankment, the settlement reduces up to 22% as compared to the condition of constant spacing to diameter ratio of encased stone columns.