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. Copyright (C) 2015, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.