This article presents the finite element modeling (FEM) based settlement analysis of two high-rise buildings founded on the stiff raft foundations 12.0 m below the ground level in Neogene clay using a modified hypoplastic model with the concept of intergranular strains. The numerical prognoses of the settlement for different phases i.e., deconsolidation, short term and long-term consolidation deformations pertaining to excavation, construction, and operation, respectively, were compared with the real-scale geotechnical monitoring (GTM) data acquired through deformeter installed in a borehole below the foundation. The results showed that the prediction of the settlement of high-rise buildings in stiff Neogene clay using the hypoplastic model can be equitable to the actual values given that calibration of model based on precisely performed laboratory tests, i.e., triaxial oedometer, simple shear and small strain element tests, high coefficient of earth pressure (K0 > 1.0) and appropriate design loads are considered for the analysis. The optimization of intergranular strain parameters showed that mR value in conjunction with r parameter affected the predicted deformation in the excavation, construction and operational phases of high-rise buildings, whereas, βr only affected the deformations during excavation and construction phases. Overall, the predictions of deformation of excavation and short-term consolidation phases using the hypoplastic model were close to the GTM as compared to that of the long-term consolidation phase, which was found to be sensitive to the contact load, σol. Moreover, in comparison to Mohr Coulomb's and cam clay models, the hypoplastic model yielded more reliable subsoil deformation for high-rise buildings based on directly calibrated parameters, proving to be a more value-added model for meticulous numerical analysis. The difference between the predictions of total settlement using the hypoplastic model for all optimization schemes was observed to be in a reasonably good range of 16–29% in comparison to the real-scale settlement.