A high-precision method to measure efficiency of fuel cells with a 0.1% margin of error is proposed. This method is principally divided into two procedures: determining the composition of fuel gas to be fed into a fuel cell system and measuring the flow rate of the fuel gas. The composition of the fuel gas is determined by an FTIR (Fourier transform infrared spectrometer) and/or a QMS (quadrapole mass spectrometer) with a built-in sonic nozzle sampling system. The flow rate was measured by the tracer gas method; that is, a given amount of tracer gas, such as one of the noble gases, was introduced into the line of the fuel gas, then, the mixed gas was sampled at the point where the tracer gas had been well mixed, and the concentration of the tracer gas was determined by the QMS. In this paper, a gravimetric calibration method using a highly sensitive balance is also proposed for flow control of the tracer gas. Also proposed are calibration of the FTIR and the QMS to establish the required low uncertainty or high accuracy of the measurement of the efficiency.