This work has the aim to carry on a techno-economic analysis to verify the performance of PEMFC and SOFC based micro combined heat and power systems, analyzing the seasonal performance of the device on the basis of the thermal and electrical 1-minute-averaged user load profiles. A Matlab® program has been written to build the annual profiles and to perform the energy evaluation of the system, considering the fuel cell production and the user demand and including a thermal and electrical storage. Four kinds of operation have been considered in order to evaluate the system behavior with different modulation strategies. Because the fuel cell needs a certain time to adapt its output power to steep load changes, a sensitivity analysis on the ramp rate has been made, in order to consider the impact of the speed of the cell in following the load requests. The calculation has been implemented both for the electrical led and thermal led operations, for single-family buildings. The economic analysis (based on the current prices of the technologies involved) has the aim to analyze different support schemes aimed at facilitating the technology competitiveness in the market, giving a general view of the possible technology applications in the near future.