Multilayered elastic structures are widely used in engineering applications. In this paper, a spectral finite element model (SFEM) is developed to predict the dynamic behavior of a multilayered beam structure. First, a higher-order multilayered beam model is derived. Each layer is modeled as a Timoshenko beam, in which both shear deformation and rotational inertia are considered. By allowing different rotation in each layer, the overall sectional warping effect is included as well. A set of fully coupled governing equations presented in a compact form and associated boundary conditions are obtained by the application of Hamilton's principle. Second, a semi-analytical solution of these equations is determined and used in formulating the SFEM. The SFEM predictions are validated against the nastran results and other results in literature. Compared to the conventional FEM (CFEM), a very small number of elements are required in the SFEM for comparable accuracy, which substantially reduce the computing time, especially for simulations of high-frequency wave propagations. Finally, the SFEM is used to predict the lamb wave responses in multilayered beams. Wave propagation characteristics in both undamaged and damaged cases are well captured. In summary, the SFEM can accurately and efficiently predict the behavior of multilayered beams and serve as a framework to conduct wave propagation prediction and damage diagnostic analysis in structural health monitoring (SHM) applications.