Perforated structures are a promising alternative to traditional breakwaters for constructing harbors and protecting coastlines. Perforated structures can effectively remove wave energy from ocean waves by the energy dissipation associated with the turbulence generated by the flow through the perforations in the structure. Understanding the factors that may affect the hydrodynamic characteristics of flow through a perforated plate is important for designing perforated marine structures. The purpose of this research was to determine the wave energy dissipation performance of thin-walled plates with various perforation configurations using OpenFOAM-based CFD simulation. Ten different plate configurations were designed and tested with a constant porosity while varying the distribution, shape, and size of the perforations, to determine the impacts to energy dissipation performance. The energy dissipation was quantified by CFD simulations of wave-interaction with a submerged perforated plate placed vertically in front of a vertical backwall (“seawall”). Physical wave flume experiments were also conducted to verify and validate the numerical models. The results showed that the perforation distribution, shape, and size play a minimal role in the energy dissipation performance when porosity is held constant. The minimal performance deviation between the perforation configurations was consistent across a range of wave periods and amplitudes.