In this paper, the seismic response analysis of deeply embedded ventilation stack is addressed by considering the effects of soil–foundation–structure interaction (SFSI). Seismic SFSI analysis of the stack subjected to a site-specific design ground motion is carried out using finite element method. A parametric sensitivity analysis is made to investigate the effect of embedment and shear wave velocity ratio of the subsurface profile on the seismic response of the stack. The first series of the SFSI analysis is carried out for the stack with surface footing using computer program SASSI 2000. The second set of analysis incorporates the effect of embedment on the seismic response of the stack. The flexible volume substructure method is used to analyze the seismic SFSI effects. It has been found that the seismic response at the various levels of the stack shows a strong dependence on stiffness of the subsurface profile and the depth of embedment. The spectral acceleration and relative displacement at the top of the stack decrease with increase in embedment ratio and these are the important parameters to be given a due consideration during design process of the stack structures.