A newly proposed three-dimensional analysis is introduced herein to estimate the foundation settlements of a vertically loaded piled raft foundation on the ground surface. Thin-plate theory with the effects of boundaries was adopted whereas alternative soil springs underneath the raft were studied for the optimal modeling. The pile-soil resistances were computed solving the equivalent stiffness of piles and surrounding soils based on the discrete wave equations. The analysis was examined with the three-dimensional finite element analysis. Although the new analysis can provide rational predictions, some significant errors were found for foundation settlements at the corner with the effects of the pile-to-pile interactions. Both discrepancies were aimed to be solved in the proposed analysis.