The impact of different parameters on the chemical degradation of the Nafion polymer electrolyte membrane was investigated in detail under different concentrations of Fenton solution. As a consequence of chemical degradation, the performance and durability of the perfluorosulfonic acid-based electrolyte membrane in fuel cells was studied. Quantitative estimation of fluoride emitted after chemical degradation of the electrolyte membrane is done by an ex-situ fluoride emission rate-test using a potentiometric with an ion-selective electrode. The concentration of fluoride ions is easily affected by several external factors, such as total ionic strength, pH, temperature, and stirring speed, which causes many errors while reporting the fluoride concentration. Furthermore, the micromorphology of recast Nafion membranes before and after FER rest was thoroughly examined by scanning electron microscope (SEM) and X-ray photoelectric spectroscopy. Here, we report the influence of several external parameters over total fluoride concentration during the estimation of fluoride concentration for the proper correlation of the rate of chemical degradation in polymer electrolytes. This systematic study is beneficial for removing errors while measuring fluoride concentration and removing the discrepancy present in FER results reported in the literature.