A class molten carbonate fuel cell (MCFC)/gas turbine combined compact system has been designed; the system has a 250-cell MCFC stack and a turbocharger generator (TCG) as part of its gas turbine. The 250-cell stack had trouble with a gas leakage; thus, a modified 125-cell stack was refabricated and operated in the system. Using the operation results of the system, the thermal efficiency was estimated for the system of the original design. The estimated thermal efficiency is 41.0% high heating value (HHV) (45.4% low heating value); the efficiency is 2% lower than the expected value of the original design. The difference of the thermal efficiency between the estimated and expected values of the 250-cell MCFC stack is due to the increase of the internal resistance caused by the stacking procedure. The 125-cell stack was operated for with the TCG and with an external air supply system at an operating current density of ; the maximum thermal efficiency of the system was estimated (43.0% HHV) at an operating current density of . The cell voltage degradation rate was converted to be at an operating current density of . The thermal efficiency, the stack performance, the temperature distribution of the stack, the performance of the TCG, etc., are discussed in detail.