A hybrid fuel cell system (~10 kWe) for an average family house including heating is proposed. The investigated system comprises a Solid Oxide Fuel Cell (SOFC) on top of a Polymer Electrolyte Fuel Cell (PEFC). Hydrogen produced from the off-gases of the SOFC can be fed directly to the PEFC. Simulations for the proposed system were conducted using different fuels. Here, results for natural gas (NG), dimethyl ether (DME) and ethanol as a fuel are presented and analysed. Behaviour of the proposed system is further investigated by comparing the effects of key factors such as utilisation factor, operating conditions, oxygen-to-carbon (O/C) ratios and fuel preheating effects on these fuels. The combined system improves the overall electrical conversion efficiency compared with standalone PEFC or SOFC systems. For the combined SOFC and PEFC system, the overall power production was increased by 8%–16% and the system efficiency with one of the fuels is found to be 12% higher than that of the standalone SOFC system.