Dynamic analysis of structures is a key challenge in structural engineering, especially in choosing effective and accurate numerical methods. Steel–concrete composite structures, commonly used in bridges and floors, require calculations of dynamic parameters to ensure safety and comfort. Few studies compare the effectiveness of the finite element method (FEM) and the rigid finite element method (RFEM) in the dynamic analysis of such structures. This study fills this gap by comparing the methods using experimental results. FEM and RFEM models were developed using Abaqus, Python, and Matlab. The main parameters were identified, i.e., the Young’s modulus of the concrete slab (EC) and the stiffness of the connection (Kx, KRX, Kv, Kh). Both methods closely matched the experimental results. The RFEM matched natural frequencies with 2–3% deviations, while the FEM showed 3–4% deviations for the torsional, axial, and first three flexural frequencies. The RFEM reduced the computation time by about 65%, making it suitable for large-scale applications. The FEM provided a finer resolution of local effects due to its higher element density. The results can be applied to the design of bridges, floors, and other structures under dynamic loads. It will also provide the authors with a basis for developing structural health monitoring (SHM).