Per- and polyfluoroalkyl substances (PFAS) are commonly used in proton exchange membrane fuel cells due to their high stability and resistance. These ionomers act as binding agents and their hydrophobic effect helps to remove excess water from the gas diffusion layer. Their proton conductivity and hydrophobicity, gained by incorporation of functional side chains, are essential features for their application as membranes.. However, the harsh conditions in fuel cells can lead to degradation of PFAS compounds, which are released into the environment. Due to their persistence, there are growing concerns about the enrichment of PFAS in groundwater and soil. As these substances accumulate in the environment, they are incorporated by living organisms through drinking water and plants. Some of these substances are associated with causing health disorders, such as cancer, brain and liver damage, and negative impacts on embryo development. This review highlights the sources of PFAS during fuel cell production, operation and recycling and currently available alternatives used in proton exchange membrane fuel cells. The degradation of fuel cells during operation has the potential to result in the emission of PFAS. Membrane degradation mechanisms have been investigated and results can serve as a foundation to reduce PFAS emissions by identifying critical operating conditions.