As the gaseous fuels interchangeability, which requires that the two gaseous fuels must be nearly identical in terms of their combustion characteristics and result in a similar engine performance, is important for internal combustion engines operation in cases of the fuel composition variation or the main fuel supply failure. In such cases, simulation tools of sufficient accuracy can be effectively employed in fuel interchangeability studies as well as for predicting the engine performance and emissions. In this study, a zero-dimensional diesel engine model is extended for simulating multi-fuel engines by considering the thermodynamic properties of the employed fuels. The model is verified against experimental data and subsequently employed to investigate the performance and knocking resistance of an SI engine operating with interchanged gaseous fuels mixtures. The derived results demonstrate that the Wobbe Index estimation is not sufficient for the characterisation of the engine performance and therefore simulation must be used for the accurate engine performance prediction with fuels interchangeability. The addition of either carbon dioxide or nitrogen results in reducing the knocking probability and retarding the knocking onset crank angle. It is inferred that the carbon dioxide addition is more effective than the nitrogen addition and concluded that the proposed model for multi-fuel engines provides results of sufficient accuracy to investigate the fuel interchangeability influence on the engine performance and knocking resistance.