Dynamic characteristics of piled raft foundation system plays an important role in the safety of high-rise buildings subjected to seismic loadings though the analytical study considering the effect of both foundation and superstructure is very few in literature. The present study first proposes an exact analytical solution for piled raft foundation subjected to harmonic excitation and resting on an elastic Winkler foundation to obtain its natural radial frequency. After successful validation through available centrifuge test results, a series of parametric study has been carried out investigating the influence of various geometrical and geotechnical parameters of the foundation and the soils respectively. It is observed that the pile length and the pile diameter has significant effect on the natural radial frequency of the foundation system whereas soil density and spacing between piles have minimal effect. The importance of stiffness of the superstructure is also considered in the proposed methodology. It is found that the natural radial frequency of piled raft foundation including superstructure stiffness decreases by 12% to 28% when compared with the computation of the natural radial frequency excluding effect of superstructure stiffness. Hence, this study provides a new analytical methodology to obtain the dynamics characteristics of piled raft foundation considering the superstructure effect which can be used for the design. •An exact new analytical solution for dynamic characteristics of piled raft is proposed.•Natural frequency of piled raft significantly altered with pile length and diameter but not with spacing.•Effect of superstructure stiffness is also considered on piled raft.•Natural frequency of piled raft decreases by about 12–28% by considering superstructure.•Influence of number of stories on natural frequency of piled raft is studied.