Based on nonlinear elastic theory and Hamilton’s principle, a generalized element stiffness matrix, which incorporates the effects of flexural as well as axial stresses induced by initial load, is given. A finite element method for dynamic analysis considering the effect of initial load is presented, with corresponding computer programs produced to facilitate the analysis. The formula is validated through a comparison in results with the analytical solution. The effects of key physical factors, including the type and magnitude of initial load, and stiffness parameters such as sectional inertia moment, inertia radius and span, on the dynamic characteristics of the beams with various restraint conditions are discussed with the effect of initial flexural stress considered. The results suggest that the natural frequency of the beam would be enhanced due to the existence of flexural stress induced by initial load and such as effect relates to the magnitude of initial load and stiffness parameters of the beam.