Adsorption with activated carbon and catalytic oxidation with an appropriate catalyst are two methods for the effective removal of gaseous dioxin-like congeners from flue gases. The removal efficiencies of chlorobenzene/chlorophenol (CBz/CPh) from gas streams achieved by an “activated carbon injection + bag filter” (ACI + BF) system in a municipal waste incinerator (MWI) and catalytic filter (CF) system installed in a pilot-scale module are evaluated in this study via sampling and analysis. Real flue gas obtained prior to activated carbon injection in the dust of an MWI is introduced and fed into a pilot-scale module to evaluate CBz/CPh removal efficiencies. The CBz and CPh removal efficiencies achieved with the catalytic filtration 180°C are 78.3% and 77.4%, respectively, and the efficiencies increase significantly with increasing temperature. Due to the different removal mechanisms of the ACI + BF and CF technologies, increasing removal efficiencies with more Cl-substituted CBz/CPh congeners in flue gas are found with ACI + BF technology as a result of higher boiling points of highly Cl-substituted CBz/CPh congeners. Thanks to the destruction of contaminants by a catalyst, relatively lower CBz/CPh concentrations (158 and 177 ng/g, respectively) were measured in the fly ash of the CF module compared with those in the ACI + BF system (301 and 371 ng/g of CBz and CPh, respectively). Since AC injection is not needed in the CF module, lower CBz/CPh contents and lower discharge of fly ash are observed compared with those seen with the ACI + BF technology. If the ACI + BF technology is replaced by CF technology, the discharge factors of CBz and CPh (including emission and fly ash) will be reduced significantly, from 11.9 and 15.3 mg/ton waste, respectively, to 6.13 and 6.11 mg/ton waste. Moreover, a reduced environmental impact is expected with the application of CF technology due to the lower CBz/CPh concentrations in fly ash compared with those seen with the ACI + BF technology.