Wankel engines were very attractive in automotive sector almost forty years ago because of small dimensions, compactness, simple design, smoothness of engine work and lack of vibration caused by inertia forces. The disadvantage of such engine was very high pollution, especially of hydrocarbons and carbon monoxide and high fuel consumption. These disadvantages can be eliminated by applying of direct injection of hydrogen and in the aviation sector by applying of fuel with high octane number also at a direct injection system. The main objective of the work is modelling of the thermodynamic process taking place during the scavenge process in such engine. At assumed geometry of the engine, initial and boundary conditions the change of engine parameters such as pressure, temperature, density, heat exchange and volume are calculated on the base of zero-dimensional model as a function of rotation angle of the piston. Forming of the mixture during fuel injection process in compression process gives information about the air excess ratio. The presented model is applicable for different sort of fuels. This work is introduction to a broader analysis of the processes in spatial system. Application of hydrogen reduces of toxic components emission from such engine, but decreases also engine power.