Today, the use of polymer electrolyte membranes (PEMs) possessing ionic liquids (ILs) in middle and high temperature polymer electrolyte membrane fuel cells (MT-PEMFCs and HT-PEMFCs) have been increased. ILs are the organic salts, and they are typically liquid at the temperature lower than 100 °C with high conductivity and thermal stability. The membranes containing ILs can conduct protons through the PEMs at elevated temperatures (more than 80 °C), unlike the Nafion-based membranes. A wide range of ILs have been identified, including chiral ILs, bio-ILs, basic ILs, energetic ILs, metallic ILs, and neutral ILs, that, from among them, functionalized ionic liquids (FILs) include a lot of ion exchange groups in their structure that improve and accelerate proton conduction through the polymeric membrane. In spite of positive features of using ILs, the leaching of ILs from the membranes during the operation of fuel cell is the main downside of these organic salts, which leads to reducing the performance of the membranes; however, there are some ways to diminish leaching from the membranes. The aim of this review is to provide an overview of these issues by evaluating key studies that have been undertaken in the last years in order to present objective and comprehensive updated information that presents the progress that has been made in this field. Significant information regarding the utilization of ILs in MT-PEMFCs and HT-PEMFCs, ILs structure, properties, and synthesis is given. Moreover, leaching of ILs as a challenging demerit and the possible methods to tackle this problem are approached in this paper. The present review will be of interest to chemists, electrochemists, environmentalists, and any other researchers working on sustainable energy production field.