The objective of this paper is to show the modelling and the transient behaviour of a natural gas desulphurising system.The plant was designed and built by Rolls-Royce Fuel Cell Systems Limited, while the plant transient model was developed and tested by the Thermochemical Power Group (TPG) of the University of Genoa, using the in-house tool TRANSEO working in the Matlab/Simulink environment. The model represents a fuel processing unit from Rolls-Royce Fuel Cell Systems Limited, designed to feed a 250kWe fuel cell hybrid system with a methane stream undergoing requirements about composition, pressure and temperature.This paper presents a simplified plant layout of the real system. In the model, physical properties of the materials and geometry of the components have been used; where no data were available, reasonable assumptions have been done.The transient model has been validated against experimental data retrieved from a 120 hours test and including warm-up, part and full load operation and cool-down phases.During the validation process both gas and wall temperatures have been considered and the transient model is shown to satisfactorily predict the plant behaviour both at steady-state and transient conditions.The model is being further developed for control system application.