The present work uses an extended high-order technique to examine free vibration analysis of Nanoscale CNTRCs sandwich beams. In this study, face sheets are made of PMMA reinforced with single-wall carbon nanotubes, and the honeycomb structure is selected for the flexible core. First-order shear deformation theory is utilized for the skins. The so-called high-order sandwich panel theory (HSAPT) is used for the core to consider the transverse shear strains in theoretical formulations. Then, skins and cores are subjected to the modified couple stress theory (MCST). For obtaining equations and related boundary conditions, the Hamilton principle is used. Additionally, three forms of beam support are examined: simply supported on both sides (SS), simply supported on one side and clamped supported on the other (SC), and clamped supported on both sides (CC). The material properties in skins are simulated to be graded in the thickness direction. The shooting method, as the numerical solution, is adopted to solve the governing differential equations to determine the natural frequencies of functionally graded carbon nanotube-reinforced composite (FG-CNTRC) beams in which boundary conditions are converted into initial conditions. Compared to other techniques, this method is a reliable way to solve complicated equations and boundary conditions; therefore, its applicability, convergence, and accuracy are verified by comparing obtained results with those existing ones in the literature. Furthermore, the influences of distribution pattern and volume fraction of carbon nanotubes, boundary conditions, the size dependency parameter, core thickness, and slenderness ratio on vibration responses are discussed. It is concluded that natural frequencies rise with an increase in skin thicknesses and length scale parameter values while decreasing when beams’ length and core thicknesses increase.