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The use of a separator to control stack temperature in a molten carbonate fuel cell was studied by numerical simulation using a computational fluid dynamics code. The stack model assumed steady-state and constant-load operation of a co-flow stack with an external reformer at atmospheric pressure. Representing a conventional cell type, separators with two flow paths, one each for the anode and cathode gas, were simulated under conditions in which the cathode gas was composed of either air and carbon dioxide (case I) or oxygen and carbon dioxide (case II). The results showed that the average cell potential in case II was higher than that in case I due to the higher partial pressures of oxygen and carbon dioxide in the cathode gas. This result indicates that the amount of heat released during the electrochemical reactions was less for case II than for case I under the same load. However, simulated results showed that the maximum stack temperature in case I was lower than that in case II due to a reduction in the total flow rate of the cathode gas. To control the stack temperature and retain a high cell potential, we proposed the use of a separator with three flow paths (case III); two flow paths for the electrodes and a path in the center of the separator for the flow of nitrogen for cooling. The simulated results for case III showed that the average cell potential was similar to that in case II, indicating that the amount of heat released in the stack was similar to that in case II, and that the maximum stack temperature was the lowest of the three cases due to the nitrogen gas flow in the center of the separator. In summary, the simulated results showed that the use of a separator with three flow paths enabled temperature control in a co-flow stack with an external reformer at atmospheric pressure.