An analytical method is developed to determine the seismic response of rotational shell structures, such as cooling towers, supported by deep foundations in the form of long piles. The substructure deletion method is employed through the development of a dynamic boundary system at the contact area between the superstructure and the substructure. A new mathematical formulation compatible with the shell deformation is developed to deal with the rigid body motions due to the negation of the fixed base assumption. Two pile foundation cases are considered in order to examine the effect of soil‐pilestructure interaction on the seismic response of cooling towers.