Clinker burning process has a decisive influence on energy consumption and the cost of cement production. A new problem is to use the process of decarbonization of alternative fuels from waste. These issues are particularly important in the introduction of a two-stage combustion of fuel in a rotary kiln without the typical reactor-decarbonizator. This work presents results of numerical studies on thermal-hydraulic phenomena in the riser chamber, which will be designed to burn fuel in the system where combustion air is supplied separately from the clinker cooler. The mathematical model is based on a combination of two methods of motion description: Euler description for the gas phase and Lagrange description for particles. Heat transfer between particles of raw material and gas was added to the numerical calculations. The main aim of the research was finding the correct fractional distribution of particles. For assumed particle distribution on the first stage of work, authors noted that all particles were carried away by the upper outlet to the preheater tower, what is not corresponding to the results of experimental studies. The obtained results of calculations can be the basis for further optimization of the design and operating conditions in the riser chamber with the implementation of the system.