Ion exchange membranes play a crucial role in water treatment, energy storage, and chemical separation. However, their efficiency is hindered by fouling, which results from the deposition of organic, inorganic, and biological contaminants, leading to increased resistance and reduced ion transport. Filtration through Ion exchange membranes relies on selective ion exchange and electrochemical gradients, while fouling mitigation requires strategic cleaning and maintenance. Cleaning methods range from physical techniques like backflushing to chemical treatments using acids, alkalis, surfactants, and enzymes. Advanced techniques, including electrochemical cleaning and nanoparticle-assisted strategies, are emerging to enhance membrane longevity and performance. This chapter discusses the working principle of ion exchange membranes, their different types, and industrial applications, particularly emphasizing membrane fouling, available cleaning strategies, and design innovation in fouling-resistant membranes.