Heterogeneous Fenton process is a kind of advanced oxidation processes (AOPs) that is significant for wastewater treatment. In the first part of this study, acid yellow 36 (AY36) degradation process has occurred in two kinds of reactors: fluidized-bed and stirred-tank reactors. Performances of these two semi-pilot reactors are compared by evaluating the removal ratio of the dye and pH changes during the process. Pyrite has been used as a heterogeneous catalyst. For obtaining the characteristics of pyrite, XRD, SEM, and FT-IR analysis have been carried out. In the second part of this study, a modified computational fluid dynamics (CFD) method has been utilized to solve the momentum and mass balances for heterogeneous Fenton process in both reactors. In AOPs, free radicals are reactive and have a short lifetime, so that turbulence mixing would be a limiting factor for the reactions that radicals are involved. By introducing a new parameter, named turbulence mixing rate, as a reaction rate for reactive species like hydroxyl radicals, the results of removal ratio and pH changes during the process showed a good agreement between the experiments and the CFD simulations, compared with not including the mixing rate in the CFD simulations (conventional kinetic modeling). In addition, the results revealed the high performance of the fluidized-bed reactor for this process in both experiments and CFD simulation. Display omitted •Fluidized-bed reactor shows better performance in contrary with stirred-tank reactor.•Turbulence mixing rate is introduced for reactive species in this process as a new parameter for CFD model.•Modified CFD model predicts pH changes and dye removal ratio simultaneously for both reactors.•Modified CFD model yield more agreement with the experiments in compared with conventional kinetic modeling.•Models are in transient state and some results are animated.