The Fenton reaction is often used to evaluate the chemical durability of polymer membranes of Proton Exchange Membrane Fuel Cells (PEMFC). However, due to the violent reaction between hydrogen peroxide and iron ions, it is difficult to compare experimental data because of low reproducibility. In this study, we tried to find the reaction conditions to improve the reproducibility of the durability test of the membrane by the Fenton reaction. The hydrogen peroxide concentration was fixed at 30%, the iron ion concentration, temperature, stirring speed, and sample size were varied, and the fluorine ion concentration of the Nafion polymer membrane deteriorated by radicals was measured. When the iron ion concentration was increased or the membrane sample size was increased, and the reaction temperature was increased to 80 °C, the experimental deviation increased, so an iron ion concentration of 10 ppm, a temperature of 70 °C, and a sample size of 0.5 cm2 were suitable.