Granular sub-base layer in flexible road pavement acts as a cushion to protect the subgrade soil under rutting. The conventional strain-based method of sub-base design limits the vertical compressive strain on subgrade based on its strength. But the strength of the subgrade reduces significantly under seismic condition. Therefore, the effect of seismic acceleration should be included for estimation of sub-base thickness in earthquake-prone area. In present paper, attempts are made to estimate the thickness of granular sub-base with change in seismic acceleration using pseudo-static approach. In present analysis, the subgrade below sub-base is considered as granular soil in a two-layered system. The subgrade CBR has been used to estimate the friction angle of subgrade soil from empirical correlation. In order to estimate vertical compressive strain on top of subgrade using Boussinesq’s theory, the two-layered system has been transformed into a homogeneous system by Odemark’s method. The change in bearing capacity factor due to change in horizontal seismic acceleration has been estimated using empirical correlations for determination of equivalent depth of soil using Odemark’s method in a two-layered system. The allowable vertical compressive strain has been estimated from IRC:37-2018 for 80% reliability criteria. The thickness of granular sub-base has been back-calculated using allowable strain and the estimated strain with reduced strength of sub-base and subgrade under seismic condition. The results obtained from present analysis closely match with the findings using IITPAVE software.