Herein, the agglomeration effect of nanoparticles on the wave dispersion of multi-scale hybrid nanocomposite beams is investigated. The constituent material consists of both macro- and nano-reinforcements which are dispersed in the polymer matrix. Homogenization is conducted according to the well-known micromechanical methods. Herein, the combination of the Eshelby–Mori–Tanaka model and the rule of the mixture is implemented in order to estimate the equivalent material properties of the nanocomposite beam. Also, a refined higher-order beam theory is used in order to calculate the kinetic relations free from utilizing an additional factor to account for the shear deformation. Furthermore, the governing equations are achieved by applying Hamilton’s principle. Then, the governing equations are solved analytically to enrich the wave frequency. The effects of various parameters on the variation in wave frequency and phase velocity of the multi-scale hybrid nanocomposite beam are studied. The results of this study reveal that the mechanical responses of the system decrease whenever the nanotubes are inside the clusters.