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Fuel‐cell‐based auxiliary power units offer power generation with reduced fuel consumption and low emissions. A very promising system is the combination of an autothermal reformer with a high‐temperature polymer electrolyte fuel cell. A fast start‐up procedure is a crucial requirement for the use of this system as an auxiliary power unit. This paper reports on the development of a suitable start‐up strategy for a 10 kWel auxiliary power unit with a start‐up burner. A commercially available diesel burner was tested as a start‐up device. A dynamic MATLAB/Simulink model was developed to analyze different start‐up strategies. With the currently available apparatus and start‐up burner it takes 2,260 s before power generation can begin according to simulation results. The fuel processor alone would be ready for operation after 1,000 s. An optimization of the fuel cell stack with regard to its thermal mass would lead to a start‐up time of 720 s. A reduction to 600 s is possible with a slight customization of the start‐up burner.