The aim of the present study was a numerical investigation of the efficiency of the combustion process of a novel concept burner under different operating conditions. The design of the burner was a part of the development process of a complete SOFC based system and a challenging combination of technical requirements to be fulfilled. A Computational Fluid Dynamics model of a non-premixed burner was used to simulate combustion of exhaust gases from the anode region of Solid Oxide Fuel Cell stacks. The species concentrations of the exhaust gases were compared with experimental data and a satisfactory agreement of the conversion of hydrocarbons was obtained. This validates the numerical methodology and also proves applicability of the developed approach that quantitatively characterized the interaction between the exhaust gases and burner geometry for proper combustion modelling. Thus, the proposed CFD approach can be safely used for further numerical optimisation of the burner design.