Fuel cell-based auxiliary power units (APUs) are a promising technology for meeting global energy needs in an environmentally friendly way. This study uses diesel containing sulfur components such as dibenzothiophene (DBT) as a feed. The sulfur tolerance of molten carbonate fuel cell (MCFC) modules is not more than 0.5 ppm, as sulfur can poison the fuel cell and degrade the performance of the fuel cell module. The raw diesel feed in this study contains 10 ppm DBT, and its sulfur concentration should be reduced to 0.1 ppm. After desulfurization, the feed goes through several unit operations, including steam reforming, water-gas shift, and gas purification. Finally, hydrogen is fed to the fuel cell module, where it generates 500 kW of electrical energy. The entire process, with 52% and 89% fuel cell and overall system efficiencies, respectively, is rigorously simulated using Aspen HYSYS, and the results are input into a techno-economic analysis to calculate the minimum electricity selling price (MESP). The electricity cost for this MCFC-based APU was calculated as 1.57$/kWh. According to predictions, the cost reductions for fuel cell stacks will afford electricity selling prices of 1.51$/kWh in 2020 and 1.495$/kWh in 2030. Based on a sensitivity analysis, the diesel price and capital cost were found to have the strongest impact on the MESP.