The behavior of stone columns in layered soil is crucial because nearly all soil deposits are heterogeneous. This study assessed the performance of an end-bearing stone column installed vertically in layered soft clay soils, consisting of a weak clay layer of varying thickness positioned on and inside a relatively stiffer clay layer. A finite element software was used to perform the numerical analyses. Results indicated that the load-carrying capacity of the stone column reinforced ground increased many folds for any thickness and positioning of the weak layer as compared to the unreinforced ground under the same loaded area. The load-carrying capacity increased by around 260% for position of the weak layer of thickness as twice the diameter of column on the stiffer layer, while for position of the weak layer of same thickness below ground surface at a depth of 0.4 times the thickness of the entire soil deposit, the limiting load-carrying capacity increased by around 320%. However, it was found that the limiting load-carrying capacity of the unreinforced and stone column reinforced ground under the same loaded area decreased with increase in the thickness of weak clay layer irrespective of the positioning of the weak layer in the layered soil deposit. The limiting load-carrying capacity of both unreinforced and stone columns reinforced ground was found to increase for the positioning of the weak layer below ground surface at greater depth inside the relatively stiffer clay layer with optimum position of the weak layer at a depth of 0.4 times the thickness of the entire soil deposit.