The precise impedance measurement system based on the well-known two-probe and four-probe methods was prepared to measure the impedance and consequent proton conductivity of Nafion membranes as standard samples, considering not only the number of electrodes and the bridging methods but also the elimination of electrical error sources for the precise electrical analysis. The proton conductivities of Nafion membranes are reported and discussed in the present study with respect to different cell configurations and measurement conditions. The values of proton conductivities measured using the four-probe method were always higher (2-5 times) than those measured using the two-probe method at ambient humidity and temperature. The proton conductivities were also measured under two different humidity conditions: water-vapor state and liquid-water state. In the water-vapor state (95% relative humidity), completely different impedance behaviors for the identical Nafion membrane were observed from the Nyquist impedance plots. All Nyquist plots derived from the two-probe method represented the inductive reactance derived from various components, such as Pt electrodes, electric conductive leads, and a potentiometer in the path of current flow rather than the capacitive reactance between Pt electrodes. The effect of contact resistance between the membrane sample and electrodes on proton conductivity was also investigated by using the two conductivity-cell configurations. It was shown that the effect of the contact resistance on the proton conductivity was more severe in the two-probe measurement, and this factor should be seriously considered in the watervapor state. Furthermore, the humidity and the temperature effects on the proton conductivity of the membranes were observed under various measuring conditions and compared with the two different cell configurations. The four-probe method well reflected the proton conductivity behavior of Nafion membrane in the wide range of temperature and humidity, as compared with the two-probe method with reasonable proton conductivity in the low humidity.