Molten carbonate fuel cells (MCFCs) are high-operating-temperature fuel cells with high efficiency and fuel diversity. Electrochemical reactions in MCFCs are exothermic. As the size of the fuel cells increases, the amount of the heat from the fuel cells and the temperature of the fuel cells increase. In this work, we investigated the relationship between the fuel cell stack size and performance by applying computational fluid dynamics (CFD). Three flow types, namely co-flow, cross-flow, and counter-flow, were studied. We found that when the size of the fuel cells increased beyond a certain value, the size of the fuel cell no longer affected the cell performance. The maximum fuel cell temperature converged as the size of the fuel cell increased. The temperature and current density distribution with respect to the size showed a very similar distribution. The converged maximum temperature of the fuel cells depended on the gas flow condition. The maximum temperature of the fuel cell decreased as the amount of gas in the cathode size increased.