Full commercialisation of the solid oxide fuel cell (SOFC) technology faces many technological challenges that prevent the incorporation of the technology into the global energy sector. The effort to increase the transient thermomechanical reliability of the interacting fuel cell components and the associated fuel cell system requires a comprehensive understanding of the complex multiphysics, occurring within the system. State of the art dynamic fuel cell system modelling comprises sub-models of the assembly, or is based on empirical nature. The present study introduces a transient, coupled 3D computational fluid dynamics/computational solid mechanics model of a complete solid oxide fuel cell system and its experimental validation. The model includes all system components; namely the fuel cell stack, afterburner, pre-reformer, air pre-heater and the auxiliary components. All components are presented in their real geometrical resolution. The capabilities of the 3D system level model are demonstrated by simulating the heating-up process and the critical system locations susceptible to thermomechanically induced stress, over time. Copyright (c) 2014, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.