Presented is a model of the dynamic deformation of a three-layer cylindrical shell with a honeycomb core, manufactured by fused deposition modeling (FDM), and skins reinforced with oriented carbon nano-tubes (CNT). A ULTEM 9085 thermoplastic-based honeycomb core is considered. To analyze the stress-strain state of the honeycomb core, a finite element homogenization procedure was used. As a result of this procedure, the dynamic response of the honeycomb core is modeled by a homogeneous orthotropic material, whose mechanical properties correspond to those of the core. The proposed model is based on the high-order theory, extended for the analysis of sandwich structures. The skin displacement projections are expanded along the transverse coordinate up to quadratic terms. The honeycomb core displacement projections are expanded along the transverse coordinate up to cubic terms. To ensure the integrity of the structure, shell displacement continuity conditions at the junction of the layers are used. The investigation of linear vibrations of the shell is carried out using the Rayleigh-Ritz method. For its application, the potential and kinetic energies of the structure are derived. Considered are the natural frequencies and modes of vibrations of a one-side clamped cylindrical sandwich shell. The dependence of the forms and frequencies of vibrations on the honeycomb core thickness and the direction of reinforcement of the shell skins have been investigated. It was found that the eigenforms of a sandwich shell are characterized by a smaller number of waves in the circumferential direction, as well as a much earlier appearance of axisymmetric forms. This means that when analyzing the resonant vibrations of a sandwich shell, it is necessary to take into account axisymmetric shapes. Changing the direction of reinforcement of the skins with CNTs makes it possible to significantly influence the frequencies of the natural vibrations of the shell, which are characterized by a nonzero number of waves in the circumferential direction. It was found that this parameter does not affect the frequencies of the axisymmetric shapes of the shell under consideration.