A diesel fuel processor for high temperature polymer electrolyte fuel cells in the 5 kW(e) power class was developed and tested. Emphasis was placed on a quick and sustainable start-up. Furthermore, operational conditions were identified that would achieve the desired reformate quality for the fuel cell anode. A thermal start-up strategy using a commercial diesel burner was developed and further optimized, resulting in a hybrid strategy with the help of a glow plug. With this strategy, self-sustaining operation of the fuel processor at full load was achieved in 27 min and the resulting reformate was of sufficient quality to operate the fuel cell in 31 min. The experimental plan includes operation periods of between 4 and 24 h with start/stop/regeneration cycles representing the daily operation of an auxiliary power unit at maximum load. With all fuels used, the target carbon monoxide concentration of 1% at the anode inlet (wet reformate) was achieved. Significant deviations from the design parameters were necessary to demonstrate a stable system performance with desulfurized Jet A-1 and to achieve the target carbon monoxide concentration with premium diesel. These results bring diesel fuel processing for auxiliary power units closer to real application, offering experimentally-validated solutions for startup and stable operation under realistic conditions with different fuels on a systems level.