A non-catalytic hydrogen generation process is provided that supplies hydrogen to a hydrodesulfurization unit and a solid oxide fuel cell system combination, suitable for auxiliary power unit application. The non-catalytic nature of the process enables use of sulfur containing feedstock for generating hydrogen which is needed to process the sulfur containing feed to specifications suitable for the solid oxide fuel cell. Also, the non-catalytic nature of the process with fast dynamic characteristics is specifically applicable for startup and shutdown purposes that are typically needed for mobile applications.