Uniform gas flow distribution in a fuel cell system is desired to attain maximum power operation potential. Two types of manifold systems are often used in fuel cell stacks; they are internal manifold system and external manifold system. This paper presents the modeling approach using the Computational Fluid Dynamics (CFD) method in analyzing fluid flow and heat transfer for the external manifold fuel cell stacks and stack module design. Computational models based on a Megawatt carbonate fuel cell stack module have been developed for investigating the fuel and oxidant flow distributions through the external manifold systems. This paper presents the modeling approaches and flow and temperature distribution results for externally manifolded fuel cell stack and stack module.