Due to the gradual and constant accumulation of seismic energy, Peninsular India (PI) is typically considered seismically stable with low to moderate seismicity. The seismic studies in Peninsular India always resorted to synthetic ground motion simulations, because of the limited instrumentation and hence lack of recorded data. In the absence of a well-defined medium model for PI, the usual practice is to use simple site proxies or one-dimensional velocity structures for ground motion simulations. However, the region consists of multi-scale geometric complexities, significant topography, and sedimentary basins and is surrounded by deep oceans. Thus, the radiated seismic wave field in the region is influenced by the medium properties and in the absence of a well-defined tomography model the reliable estimation of seismic hazard is a challenging problem in PI. Therefore, the seismic wave propagation in PI can be investigated using numerical simulation with reliable 3D computational model for PI, incorporating the knowledge of the underlying Earth structure. Hence, the present study attempts to develop a sophisticated three-dimensional (3D) medium model of Peninsular India for physics-based ground motion simulations for regional earthquakes. This is aided by the availability of one-dimensional (1D) velocity models and the crustal structure from the receiver function analysis which provides valuable insight into the variation of material properties in the region. In the present study, >100 s of 1D velocity profiles are collected from various literature, which is then grouped under 23 different geological regions identified in PI (as per GSI (2000)). The averaged material properties are assigned per each geological region and the information on sediment depths, basin geometry, topography, and bathymetry are incorporated. We use the spectral element method (SEM) to calibrate our 3D computational model by simulating synthetic seismograms and comparing them to recorded ground motions for two past earthquakes: the 2001 Mw 7.6 Bhuj earthquake and the 1997 Mw 5.8 Jabalpur earthquake. Further, the seismic waveforms at the near field of 2001 Mw 7.6 Bhuj event are simulated using a refined regional model. The spatial variability of associated seismic intensities and peak ground velocity (PGV) amplification are investigated. In addition, a study of the impact of model depth truncation and sphericity on ground motion is also conducted. The implemented medium model is the first of its kind for Peninsular India and can reliably be used in seismic wave propagation studies in the region. The simulated outcomes from the model are of engineering importance as these results can be used for seismic hazard assessment of the region.