The pressure losses at manifold junctions in a molten carbonate fuel cell (MCFC) stack depend on the stacking positions of the cells and the flow rate in the manifold. These pressure losses affect the uniformity of gas flow rate in each stacked cell and consequently also affect the cell performance. In this study, the pressure losses at dividing and combining junctions in a plate heat-exchanger type MCFC stack were examined by numerical analysis. A stack consisting of 100 cells was assumed, and the junction pressure losses at various stacking positions of cells were calculated under various flow rate conditions ranging from the minimum possible flow rate (80% utilization of fuel gas) to the maximum possible flow rate (10% utilization of oxidant gas). The results were arranged according to the equations for loss coefficients, and were compared with the experimental results of previous studies.