Stone columns consist of granular material compacted in long cylindrical holes. They are used for improving the strength and consolidation characteristics of compressible soils. However, they are still less effective at supporting heavy loads, since they still cannot transfer applied stresses to deeper layers of soil. The main objective of this numerical study was to investigate the geotechnical performance of a combined foundation system composed of stone columns and piles grouped together under a rigid raft foundation in compressible soil. The failure mechanism of this hybrid foundation system was examined, and configurations optimizing the performance of the combined foundation system were explored. An analytical model was developed for predicting the ultimate carrying capacity of the combined system in compressible soils. It was deduced that combining stone columns and piles in one foundation system improved considerably the system’s carrying capacity. Moreover, the uppermost improvement was observed when the piles were installed on the periphery or edge of the raft foundation, while stones columns were placed at the center area of the raft. The failure of the combined foundation system started from the center of the raft and noticeably extended to its edges. Due to the presence of stone columns in the combined foundation system, the piles did not interact. The areas affected or influenced by the soil–pile interaction also did not overlap.