Utilization of graphene covered waveguide inserts to form tunable waveguide resonators is theoretically explained and rigorously investigated by means of full-wave numerical electromagnetic simulations. Instead of using graphene-based switching elements, the concept we propose incorporates graphene sheets as parts of a resonator. Electrostatic tuning of the graphene surface conductivity leads to changes in the electromagnetic field boundary conditions at the resonator edges and surfaces, thus producing an effect similar to varying the electrical length of a resonator. The presented outline of the theoretical background serves to give phenomenological insight into the resonator behavior, but it can also be used to develop customized software tools for design and optimization of graphene-based resonators and filters. Due to the linear dependence of the imaginary part of the graphene surface impedance on frequency, the proposed concept was expected to become effective for frequencies above 100 GHz, which is confirmed by the numerical simulations. A frequency range from 100 GHz up to 1100 GHz, where the rectangular waveguides are used, is considered. Simple, all-graphene-based resonators are analyzed first, to assess the achievable tunability and to check the performance throughout the considered frequency range. Graphene–metal combined waveguide resonators are proposed in order to preserve the excellent quality factors typical for the type of waveguide discontinuities used. Dependence of resonator properties on key design parameters is studied in detail. Dependence of resonator properties throughout the frequency range of interest is studied using eight different waveguide sections appropriate for different frequency intervals. Proposed resonators are aimed at applications in the submillimeter-wave spectral region, serving as the compact tunable components for the design of bandpass filters and other devices.