Fuel cells with nominal outputs of approximately 1kW AC are emerging as a prime-mover of a micro-cogeneration system potentially well-suited to compete, on an energy basis, with conventional methods for satisfying occupant electrical and thermal demands in a residential application. As the energy benefits of these systems can be incremental when compared to efficient conventional methods, it is especially important to consider the uncertainties of the models on which simulation results are based. However, researchers have yet to take this aspect into account.This article makes a contribution by demonstrating how these model uncertainties may be propagated to the simulation results of a micro-cogeneration system for comparison to a reference scenario using a case study. This case study compares the energy performance of a fuel-cell based micro-cogeneration system serving only domestic hot water demands to an efficient reference scenario where the conventional methods for providing electrical and thermal demands are considered to be a central gas-fired combined-cycle plant and a condensing tankless water heater respectively. The simulation results demonstrated that if model uncertainties were ignored, it would have been possible to demonstrate that the considered micro-cogeneration system was more efficient than the reference scenario for average consumption levels of domestic hot water. However, when model uncertainties were considered, the efficiency of the considered micro-cogeneration system could not reliably exceed that of the reference scenario by serving the domestic hot water needs of a single-family home.