Polymer electrolyte membrane (PEM) electrolyzers are renewable energy storage systems that produce high purity hydrogen fuel from electrochemical water splitting. The PEM in particular is a key component that acts as a solid electrolyte between electrodes and separates the reactants, but despite these benefits, its internal ion transport mechanisms are not fully understood. Here, the first microfluidic PEM electrolyzer that is semi-transparent in the infrared (IR) spectrum is developed as a platform for characterizing the PEM hydration during operation. The electrochemical performance of the chip is compared to its PEM hydration, which is measured via synchrotron Fourier-transform infrared (FTIR) spectroscopy. The PEM water content is directly probed in the operating electrolyzer by measuring the transmitted light intensity at wavelengths around 10 μm. By supplying the electrolyzer with reactant starving flow rates, mass transport driven cell failure is provoked, which coincides with membrane dehydration. Furthermore, higher operating temperatures are observed to improve the stability in membrane hydration through increasing the membrane water uptake. The methods presented here prove the viability of IR techniques for characterizing membrane hydration, and future extension towards imaging and thermography would enable further quantitative studies of internal membrane transport behaviors.