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This paper presents a boundary element method to analyze the elastic foundation finite beams on 2D plane-strain and 3D multilayered isotropic soils. Starting with the basic equations of elasticity and based on the Fourier transform, the transfer matrix of a single soil layer is derived. According to the boundary conditions and continuity conditions between two adjacent soil layers, the solution of multilayered elastic soils is obtained to be a kernel function of BEM analysis. The elastic foundation beam is modeled as a Bernoulli-Euler beam using the finite difference method. With the displacement and stress condition of coordination between beam and soil, the solution is acquired for beams resting on multilayered soils. Comparing the solution with the published data shows that the solution is in good agreement, and some numerical examples show that the beam behavior is affected vitally by soil-beam stiffness ratio and the stratification of soils.