Depending on specific configuration and design, a variety of physical phenomena is present in fuel cells, e.g., multi-component gas flow, energy and mass transfer of chemical species in composite domains and sites. These physical phenomena are strongly affected by chemical/electrochemical reactions in nano-/micro-scale structured electrodes and electrolytes. Due to the electrochemical reactions, generation and consumption of chemical species together with electric current production take place at the active surfaces for all kinds of fuel cells. Furthermore, water management and twophase flow in proton exchange membrane fuel cells (PEMFCs) and internal reforming reactions of hydrocarbon fuels in solid oxide fuel cells (SOFCs) are strongly coupled with the electrochemical reactions and other transport processes to make the physical phenomena even more complicated. For modeling and analysis at the unit-cell and component level typically CFD-based approaches might be appropriate. On the fuel cell stack and system levels, methods like lumped parameter analysis and overall energy/mass balances are more suitable. This paper describes the various kinds of methods for modeling and analysis, and how these can be used as well as their applicability and limitations.