This paper employs a surface stress-driven nonlocal theory to investigate the synergistic impact of long-range interaction and surface energy on higher vibration modes of Bernoulli–Euler nanobeams made of functionally graded material. It takes into account surface effects such as the surface modulus of elasticity, residual surface stresses, surface density, and rotary inertia. The governing equation is derived through the application of Hamilton’s principle. The novelty of this work lies in its pioneering approach to studying higher-order vibrations, carefully considering the combination of long-range interactions and surface energy in nanobeams of functionally graded materials through a well-posed mathematical model of nonlocal elasticity. This study conducts a parametric investigation, examining the effects of the nonlocal parameter and the material gradient index for four static schemes: Cantilever, Simply-Supported, Clamped-Pinned and Clamped-Clamped nanobeams. The outcomes are presented and discussed, highlighting the normalized nonlocal natural frequencies for the second through fifth modes of vibration in each case under study. In particular, this study illustrates the central role of surface effects in the dynamic response of nanobeams, emphasizing the importance of considering them. Furthermore, the parametric analysis reveals that the dynamic response is influenced by the combined effects of the nonlocal parameter, the material gradient index, the shapes of the cross-sections considered, as well as the static scheme analyzed.