This study investigated the polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/Fs) removal efficiencies in two medical waste incinerators (MWIs) -MWI-A and MWI-B, with waste burning capacities of 9.12 and 12 tons per day, with dual-and single-bag filter systems, respectively. The PCDD/Fs in the stack flue gas and fly ashes of each air pollution control device (APCD) unit were collected concurrently. Based on mass balance, it was determined that the major PCDD/F removal occurred in the bag filter system with activated carbon injection (ACI). The total PCDD/F emission removal efficiencies for the whole dual-bag filter system, bag filter 1 (BF1), bag filter 2 (BF2) in MWI-A and the single bag filter system (BF) in MWI-B were 99.7%, 84.8%, 98.0%, 99.0% on the mass basis, respectively. The PCDD/F emission ratio (the escaped PCDD/F ratio after all APCDs) with the dual-bag filter system was over four times lower than that with a single bag filter. The results demonstrate a very efficient way to reduce the excess PCDD/F emissions incurred by intermittent operations and irregular waste feeding.