With the forecasted increase in the construction and operation of nuclear reactors, there will be a corresponding increase in the quantity of spent nuclear fuel (SNF) that requires long-term storage. In SNF, transuranic isotopes contribute the most to the long-term radiotoxicity of the fuel and pose a proliferation risk. One option that has been explored to address these issues is the removal of the transuranic isotopes from SNF and the conversion of these isotopes into transuranic fuel (TRU fuel). This work sought to determine how effective a micro-modular Pebble-Bed High-Temperature Gas-Cooled Reactor (PB-HTGR); the 10-MW High Temperature Gas-cooled Test Reactor (HTR-10); and a salt-cooled small-modular pebble-bed reactor (PBR), i.e. the generic Fluoride-cooled High-temperature Reactor (gFHR), are at reducing the inventory of transuranic isotopes while still maintaining the intrinsic safety features of the PBR designs, such as negative temperature coefficients of reactivity. Optimized pebble designs utilizing TRU fuel were found for both reactors through the adjustment for the packing fraction of fuel in each pebble. The Axial Zone Equilibrium Modeling (A-ZEM) method was used in this work to help select the optimized pebble design. Once an optimized pebble design was selected and an equilibrium model was produced, the results from the deep burn (DB) HTR-10 and gFHR designs were compared to the results of two models from the literature. While both the DB gFHR and the DB HTR-10 were able to reduce the weapons-usable transuranic inventory, the performance of these reactors did not match that of the small-modular PB-HTGRs in the literature. Therefore, a need was identified for further refinement of the gFHR design using TRU fuel, as the results for this model were more promising than those of the DB HTR-10, which was strongly limited by the high leakage intrinsic to micro-modular PB-HTGRs.