A fuel cell generates electricity cleanly and efficiently by utilizing the chemical energy contained in hydrogen or other fuels. Fuel cells are remarkable in their application versatility; they may be used for a wide range of systems, from huge utility power plants to mobile phones, and they can operate on a wide variety of fuels and feedstocks. Current fuel cell systems are still inefficient to be commercially viable, as cost, performance, and durability remain important challenges in the fuel cell industry. As a key component in fuel cells, polymer electrolyte membrane (PEM) provides channels for ion transport and prevents fuel crossover, which plays a critical role in improving performance and lowering the cost of the fuel cell. This chapter discusses the polymer electrolytes used in fuel cells, specifically proton-exchange membrane fuel cell (PEMFC) and anion-exchange membrane fuel cell (AEMFC) systems, as well as their characteristics. The two most extensively used polymer electrolyte for PEMFC and AEMFC applications, respectively, are perfluorosulfonic acid ionomers, represented by Nafion, and quaternary ammonium-functionalized hydrocarbons, represented by Tokuyama A201. Their ion transport mechanisms and methods of preparation are introduced. Along with the many other types of materials being investigated as potential PEM, strategies for overcoming major challenges and developments in ion-exchange polymer electrolytes are presented.