We have proposed a new method to accurately predict the resonance of Fabry-Perot Cavity (FPC) antennas enclosed with conducting side walls. When lateral directions of an FPC antenna are not blocked with metallic walls, the conventional technique is accurate enough to predict the resonance of the FPC antenna. However, when the FPC antenna has side walls, especially for case with only a short distance between the walls, the conventional prediction method yields an inaccurate result, inevitably requiring a tedious, time-consuming tuning process to determine the correct resonant height to provide the maximum antenna gain in a target frequency band using three-dimensional full-wave computer simulations. To solve that problem, we have proposed a new resonance prediction method to provide a more accurate resonant height calculation of FPC antennas by using the well-known resonance behavior of a rectangular resonant cavity. For a more physically insightful explanation of the new prediction formula, we have reinvestigated our proposal using a wave propagation characteristic in a hollow rectangular waveguide, which clearly confirms our approach. By applying the proposed technique to an FPC antenna covered with a partially reflecting superstrate consisting of continuously tapered meander loops, we have proved that our method is very accurate and readily applicable to various types of FPC antennas with lateral walls. Experimental result confirms the validness of our approach.