This study presents a comparative evaluation of Molten Carbonate Fuel Cell (MCFC) and Solid Oxide Fuel cell (SOFC) stacks coupled with a micro gas turbine (MGT). For the analysis, it is assumed that the fuel supply to the stacks is constant in all the analyzed conditions. The components of the system have been sized using the first law of thermodynamics to meet the thermal conditions required to maintain fuel cell stack operation, while an exergetic analysis has been implemented in order to assess the components in terms of irreversibilities. Furthermore, an economic analysis to estimate the Levelized Cost of Electricity (LCOE) has been carried out to indicate the most feasible option between the two analyzed systems. The capacity of the fuel cell stacks is 500kWdc operating at 350 kPa and 600 degrees C/650 degrees C. The results indicate that MCFC stacks are more efficient than SOFC stacks, but are considerably more expensive. Nevertheless, the SOFC/MGT system has a global ef-ficiency higher than that of the MCFC/MGT; also its Total Capital Investment (TCI) is 2.5-3.5 times lower, thus making the SOFC/MGT coupling more attractive. The only product considered coming out from the systems to determine the LCOE is electricity. The LCOE for the SOFC/MGT system is 0.339-0.402$/kWh and for the MCFC/MGT is 0.875-0.897$/kWh, which for both configurations is still higher than the current electricity prices. One aspect that increases the investment and consequently the LCOE is the high cost of the stacks and their replacements which is around 19 % and 10 % of the total Purchased Equipment Cost (PEC) for MCFC and SOFC stacks, respectively.