The nonlinear frequencies of pre-stressed graphene-based structures, such as flat graphene sheets and carbon nanotubes, are calculated. These structures are modeled with a nonlinear hyperelastic shell model. The model is calibrated with quantum mechanics data and is valid for high strains. Analytical solutions of the natural frequencies of various plates are obtained for the Canham bending model by assuming infinitesimal strains. These solutions are used for the verification of the numerical results. The performance of the model is illustrated by means of several examples. Modal analysis is performed for square plates under pure dilatation or uniaxial stretch, circular plates under pure dilatation or under the effects of an adhesive substrate, and carbon nanotubes under uniaxial compression or stretch. The adhesive substrate is modeled with van der Waals interaction (based on the Lennard-Jones potential) and a coarse grained contact model. It is shown that the analytical natural frequencies underestimate the real ones, and this should be considered in the design of devices based on graphene structures. 1 identity tensor in R 3 co-variant tangent vectors of ; = 1, 2 co-variant components of the metric tensor of contra-variant components of the metric tensor of contra-variant tangent vectors of ; = 1, 2 0 reference configuration of the manifold current configuration of the manifold co-variant components curvature tensor of (0) logarithmic surface strain (0) dev deviatoric part of the logarithmic strain Γ Christoffel symbols of the second kind mean curvature of surface area change of 1