This article describes a method for calculating the frequency sensitive dynamic stiffness of the soil base using the finite element method. The main advantage of the method is the ability to take into account the heterogeneity of the properties of the base when calculating dynamic stiffness. Requirements for creating a design model, special boundary conditions, size and type of finite elements, and processing of results are presented. Based on the calculation results, a comparison with standard dynamic stiffnesses was made. It is shown that due to the presence of layering in the base, the standard and numerical dynamic stiffness have significant discrepancies. A solution to the test problem of determining the dynamic stiffness for a rectangular stamp on a layered base is presented. A comparison of the calculation results with a known solution shows the acceptable accuracy and reliability of the solution and confirms the correctness of the proposed calculation method.