Fuel cells are processes of electric and thermal energy production which can be used for electric vehicles. They deliver strong power densities and do not require load time as batteries do. However, the use of fuel cells introduces strong constraints related to their different parts: feed systems, conversion and storage of fuel (hydrogen or methanol), management of the produced energy either under electric or thermal form, discharge of exhaust gases. The risk analysis presented in this paper consists of forecasting and minimizing undesired events that could occur when a fuel cell is powering an electric vehicle. This study refers to electric vehicles based on relevant fuel feeds (e.g., hydrogen or methanol). The MADS/MOSAR methodology is used. Five scenarios of accident are highlighted, leading to jet flame, BLEVE, internal combustion, unconfined explosion and environmental pollution. They are evaluated and prioritized by using Severity versus Probability grid. The main risk in terms of both severity and probability is related to fuel handling that can be nevertheless limited by using prevention and protection barriers. Due to the low durability of the electrolyte, the risk of electrolyte failure can be also very important.