Introduction Waste incineration is a well-established treatment technology for municipal, industrial, hospital and hazardous wastes [1–3]. It is also one of the most frequently selected method of waste management for no-longer reusable or recyclable industrial products and materials [4–8]. In the some part of waste incinerators, persistent organic pollutants (POPs) are formed due to the presence of products of incomplete combustion, oxygen and chlorine at temperatures between 200 and 800 °C [9, 10]. The final solution for persistent organic pollutants (POPs) such as polychlorinated biphenyls (PCBs) that cannot be recycled or landfilled is to use an incinerator [11]. The minimum residence time suggested for removal of PCBs in an incinerator is about 2 s at 1200 °C or 1.5 s at 1600 °C [11]. This can be achieved only through increasing the residence time or improved heat distribution. Measurements indicate that most PCBs incinerators are not able to provide these conditions due to the presence of inefficient cold zone with low efficiency in terms of mixing and heat distribution [12, 13]. Furthermore, in the cold zone of waste incinerators polychlorinated biphenyls (PCBs) are formed [10, 14–16]. In recent years, many attempts have been made to model processes in incinerators. San José et al., investigated the effect of incinerator efficiency on the emissions in an industrial area with the help of MM5, CMAQ and EMIMO [17]. The results showed that the effect of emissions from incinerator is insignificant compared to the surrounding industries and highways. The effect was comparable just in the case of ozone. Stanmore et al., modeled the formation of PCDD/F in municipal and hospital incinerators and proposed a general empirical model to calculate the level of gaseous and solid PCDD/F [18]. In another study, Goh et al., modeled the combustion bed of a municipal incinerator and proposed a comprehensive flexible model [19]. The results of the model were used as boundary conditions for modeling upper gases in CFD models. The model results can also be used to optimize the incinerator and reduce the production of waste sludge and waste mixing [19]. In a similar study, the waste mixing was modeled before burning in an incinerator. In this study, a mathematical model was proposed for simulating waste mixing in the incinerator and the model results were compared with experimental results. Huang, used a kinetic model of reaction to model the formation PCDD/F in an industrial incinerator [20]. The model variables include the formation and removal rates of PCDD/F, carbon gasification, partial pressure of oxygen and equations for temperature and time. A good agreement was obtained between the experimental and model results. Khiari et al., proposed a mathematical model for dynamic simulation of an incinerator [21]. The lower part of the incinerator and waste pyrolysis were modeled. The model results were compared with the results of similar studies. Thomas offered an one-dimensional model to simulate the incineration of emissions in an incinerator [22]. Taking into account radiation, convection and conduction heat transfer processes, and the gas flow was simulated. The heat capacity of gases, thermal conductivity and viscosity effects were included considering the temperature dependence of the reaction. The main objective of this study was to investigate the explores ways to optimize the efficiency of the PCBs removal in incinerators in the presence of baffles embedded in the combustion chamber. Modeling was performed first with 2 and then with 3 baffles.