Abstract This work deals with the theoretical and experimental analysis of fuel-cell-based auxiliary power units operated with reformate from diesel and kerosene reforming for trucks and aircraft. In the theoretical part, a PEFC and an HT-PEFC system were analyzed using process simulation software. In the experimental part, a fuel processor consisting of an autothermal reformer, a water-gas shift reactor and a catalytic burner with 28 kW thermal power was characterized using different diesel and kerosene fuels. These fuels included desulfurized Jet A-1 and Aral Ultimate diesel as petroleum-based fuels and GTL kerosene, GTL diesel (winter and summer grades) and BTL diesel as non-petroleum-based synthetic fuels. The PEFC system showed a calculated electrical net efficiency of 28.5%, whereas 22.3% was calculated for the HT-PEFC system. A high-quality reformate was produced using various diesel and kerosene fuel qualities in the reformer with a relevant technical power class for the APU application. Although a performance loss of the shift reactor was observed, it was kept at an acceptable level at the end of experiments.