To support and inform the design process of a 1MW SOFC system, Rolls-Royce Fuel Cell Systems (RRFCS) is developing software simulations of the various physical system configurations involved, and building them together towards a collective understanding of the system behaviour. Thermal network models, computational fluid dynamics models and stress models are related and their temperature fields in particular are coupled as temperatures required for optimum operation have significant impact on the mechanical integrity and behaviour of the fuel cell stack and other components.This paper describes the disparate modelling work that has been required for the development of the RRFCS prototype demonstration of a 250kW generator module. The contribution and interaction of the modelling strands is shown by examples, together with the establishment of confidence in the system design in terms of integrity and reliability. SOFCs present a unique set of challenges in terms of thermal management, fluid dynamics, and material stresses, and these are each individually and collectively addressed by appropriate supporting modelling work.