This study focuses on the evaluation of the performance of a rectangular waveguide for deep hyperthermia when different antennas are used. Although there are several models of hyperthermia applicators, there are no studies of the advantages of employing different antennas for waveguides used in deep seated tumor treatments. Monopole antennas are the most used radiating elements inside waveguides. Here, the modeling of a monopole and two new proposed antennas, inverted T and plate, in order to find their optimal performance is presented. Parameters like output power, SWR and transmission coefficient generated for each modeled antenna were calculated by using the finite element method. The antennas with the best performance were selected in order to model an applicator-phantom system, which was used to calculate the temperature distributions generated inside the muscle phantom. The models were based on Maxwell and bioheat equations. Finally, thermal distributions were obtained and compared. The results indicate that the plate antenna generated a better focusing. The SWR obtained was 1.25, the output power was 54.71 W of 66 W applied, and the 42 • C isotherm had a size of 2 cm × 2 cm.