The present study investigates the surface energy of metallic nanoplates as the most basic thermodynamic concept of nanostructures using one of the most efficient available computational tools in the field of nanoscience i.e. the molecular dynamics simulations. Whenever physicochemical properties of nanostructures are discussed, the surface energy is one of the key parameters. This parameter has the utmost importance at nanoscale since at this scale the surface to volume ratio is very large and thus there is a significant difference between nanoscale properties and the engineering scale properties. In this study, the surface energy of gold and silver metallic nanoplates using molecular dynamics simulations are investigated and shown to be dependent on size. The surface energy of metallic nanoplates with different thicknesses were calculated and it was shown that for very thin metallic nanoplates with sufficiently small thickness in the order of a few nanometers, the surface energy is dependent on the thickness of nanoplate and the surface energy decreases by reducing the thickness of the nanoplate. By analyzing the excess energy of different layers in very thin nanoplates, it was found that this size-dependent behavior is due to the reduction of excess surface free energy density in surface layers and its increase in the inner layers that overall reduces the surface energy of nanoplate.