The proton conductivity of a polymer electrolyte membrane has been measured in the film thickness direction by employing an Au/polymer electrolyte membrane/Au sandwiched cell by varying the electrode area, pressure of the sandwiched cell, and applied voltage. As a result, the optimized electrode area, gauge pressure and applied voltage were found to be 0.015–0.070 cm2, 0.8–1.5×105 Pa, and 10–50 mV, respectively. By using Nafion 117 as a polymer electrolyte membrane, we measured the proton conductivity in the film thickness direction and compared it to that in the film surface direction evaluated by a conventional four-probe method, which resulted in the same magnitude of 0.090 S cm−1.