In this work, the behavior of a graphene-based capacitor was investigated by using an electromagnetic (EM) simulator. The graphene electrodes were simulated as a porous structure with a varying pore diameter as derived from experimental data. The main issue in modeling such a structure is the large number of objects with nano- or micro-dimensions (∼millions), which imposes a significant computation challenge for the simulator. A solution was developed by introducing an externally created matrix of the electrode with a fixed number of elements, which allowed the successful and accurate simulation of the complex porous-based structure. The pores of the electrodes are modeled as cylindrical holes in a solid graphene parallelepiped, while the capacitance is determined for different dimensions of pores of electrodes with a corresponding shape of the dielectric medium. The results obtained show a significant increase in the capacitance compared to a capacitor with flat metal electrodes.