Present paper is proposed to capture the influences of carbon nanotubes’ agglomeration on the stability behaviors of multi-scale hybrid nanocomposite beams within the frameworks of refined higher order beam theories for the first time. In this research, a mixture of macroscale and nanoscale fillers will be utilized to be dispersed in an initial matrix to possess a multi-scale hybrid nanocomposite. The equivalent material properties are seemed to be calculated coupling the Eshelby–Mori–Tanaka model with the rule of the mixture to consider the effects of carbon nanotubes inside the probably generated clusters while finding the mechanical properties of such novel hybrid nanocomposites. Furthermore, an energy-based approach is implemented to obtain the governing equations of the problem utilizing a refined higher order beam theorem. Next, the derived equations will be solved in the framework of Galerkin’s well-known analytical method to reach the critical buckling load. It is worth mentioning that influence of various boundary conditions is included, too. Once the validity of presented results is proven, a set of numerical examples are presented to explain how each variant can affect the structure’s stability endurance.