The catalytic oxidation of trace organic compounds generated from waste incineration is usually carried out by a fixed-bed reactor. However, the performance of a fluidized catalyst reactor is seldom studied. This work investigated the destruction removal efficiency (DRE) of benzene, toluene, ethylbenzene, xylene (BTEX), and polycyclic aromatic hydrocarbons (PAHs) generated from waste incineration under different operating conditions by a fluidized palladium catalyst. The investigated conditions included different fluidized velocities and the effects of heavy metals, acid gas, and water vapor. Experimental results showed that the fluidized-catalyst reactor was very effective for destroying BTEX and PAHs and capturing particles. When the feedstock contained heavy metals, Pb and Cd inhibited the oxidation of organic compounds, but Cr did not. Because the feedstock contained sulfur and chloride (PVC), the palladium catalyst was poisoned and deactivated. The presence of water vapor also decreases the DRE of BTEX and PAHs. Moreover, the particle size distribution of fly ash and heavy metals after the catalyst reactor became smaller by comparing the mass size distribution of fly ash and the elemental size distribution of heavy metals (Pb, Cr, Cd) before and after the fluidized-catalyst reactor.