In this study, we performed numerical simulation of the adsorptive desulfurization reactor for a 100 kW fuel cell. Using experimental results and the adsorption kinetics theory, the adsorption rate of sulfur in diesel was estimated and verified by numerical analysis. By analyzing the performance of desulfurization according to reactor size, the optimal reactor size was determined. By maximizing processed diesel amount, optimal diesel flow rate was determined. Regeneration process was also confirmed for the obtained optimal reactor size. The present work will be utilized to design a diesel desulfurization reactor for a fuel cell used in a ship by further process modeling and economic analysis.