Fuel cell supplied auxiliary power units could ease the development of fuel cell systems in transportation application if they are fed by conventional hydrocarbons like diesel. Then a fuel processor has to be used to convert the hydrocarbon in a hydrogen rich gas mixture with a low rate of contaminant. The temperatures of the fuel processor modules and the mass flows have to be controlled. The energetic macroscopic representation (EMR) is a causal, graphic modeling tool for complex multi-domain systems that can be used for the design of the control structure through the inversion of model. in this work EMR is used to model a diesel supplied low temperature fuel cell unit including the fuel processor, the fuel cell stack (HTPEM) as well as the supply system of the mass flows. The presented fuel processor and HTPEM models are validated against experimental results. The structure of the temperature and mass flow controls in the fuel processor and supply system are derived. Both the model and the control are implemented in Matlab/Simulink (TM) and validated. (C) 2009 Professor T. Nejat Veziroglu. Published by Elsevier Ltd. All rights reserved.