In this paper, the control system for a catalytic afterburner in a diesel fuel cell auxiliary power unit is presented. The catalytic afterburner is used to burn the non-utilised hydrogen and other possible combustible components of the fuel cell anode off-gas. To increase the energy efficiency of the auxiliary power unit, the thermal energy released in the catalytic afterburner is utilised to generate the steam for the fuel processor. For optimal operation of the power unit in all modes of operation including load change, stable steam generation is required and overall energy balance must be kept within design range. To achieve this, the reaction temperature of the catalytic afterburner must be stable in all modes of operation. Therefore, we propose the afterburner temperature control based on mass and thermal balances. Finally, we demonstrate the control system using the existing prototype of the diesel fuel cell auxiliary power unit. (C) 2016 Elsevier B.V. All rights reserved.