The paper describes modelling of spray drying system where valved and valveless pulse combustors were applied as a source of drying agent. Experimental analysis of pulse combustors operation was carried out in order to optimize their performance to achieve low emission of toxic substances, stable operation and high and smooth pressure oscillations. Optimized valved and valveless units were applied in the drying system. Extensive drying and evaporation tests were carried out to establish basic data required for modelling of the system. Laser techniques were applied to determine flow field in the drying chamber (LDA) as well as to analyse the structure of disperse phase (PDA). A modified mathematical model of heat, mass and momentum transfer in spray drying, developed earlier, was used to describe the pulse combustion drying system. The model enables to obtain temperatures of continuous and disperse phases, percent of evaporation and positions of particular fractions in the dryer. Air velocity profiles in the axial and radial directions in the drying chamber determined experimentally were substituted to the main programme calculating the spray drying process. A comparison of theoretical and experimental results shows good agreement also for complex hydrodynamics of pulsating flow in the drying chamber. Experimental investigations and mathematical modelling proved that the pulse combustion spray drying system could be effectively applied in dewatering of solutions with low content of solids, which could be important for waste disposal.