The present work proves by both simulation and experimental work that the most common empirical formulas available in the previous publications for the design of substrate-integrated waveguide (SIW) cavities are incorrect in most cases. Moreover, the present work provides correct and exact design equations that are examined by both simulation and experimental work. In planar circuit structures, rectangular waveguide and resonators are commonly integrated within a dielectric substrate to produce what is known as SIW structures. For ease of fabrication and embedding into the dielectric substrate, the closed (solid) side walls of the rectangular waveguides and resonators are replaced by metallic via arrays. The main concern of the present paper is to investigate the effects of such replacement on the performance of a SIW resonator through simulation as well as experimental work. The limiting constraints on the relative dimensions of such via arrays including the diameter of the vias and the spacing between them are numerically and experimentally investigated to ensure proper operation of the SIW resonator regarding the radiation loss due to leakage from the openings of the resonator side walls. The effects of the via array dimensions on the resonant frequency, radiation loss, and quality factor (Q-factor) of the resonator are evaluated. For this purpose, two models of the rectangular resonator embedded in the dielectric substrate are designed to operate at 10 GHz. The first model is an ideal box-shaped resonator of solid sidewalls whereas the other model is a conventional SIW resonator with via-array side walls. The two types of the substrate-embedded resonators are fed through a microstrip line. The resonant frequency, losses, and Q-factor of the two resonator models are compared to each other taking the box-shaped resonator as a reference because of its ideal structure to evaluate the performance of the conventional SIW resonator. The two types of resonator are fabricated for comparison through experimental measurements. The empirical design equations that are commonly available in literature to calculate the effective dimensions of the SIW resonator are investigated by comparison with the exact simulation results and shown to be incorrect in most cases. More accurate and reliable design equations are proposed in the present work. The results of the proposed design equations are compared to the simulation results showing excellent accuracy and shown to be more reliable than those available in literature.