A solid oxide fuel cell (SOFC) system consists of a fuel cell stack with its auxiliary components. Modelling an entire SOFC system can be simplified by employing standard process flowsheeting software. However, no in-built SOFC module exists within any of the commercial flowsheet simulators. In Amiri et al. (Comput. Chem. Eng., 2015, 78:10-23), a rigorous SOFC module was developed to fill this gap. That work outlined a multi-scale approach to SOFC modelling and presented analyses at compartment, channel and cell scales. The current work extends the approach to stack and system scales. Two case studies were conducted on a simulated multilayer, planar SOFC stack with its balance of plant (BoP) components. Firstly, the effect of flow maldistribution in the stack manifold on the SOFC's internal variables was examined. Secondly, the interaction between the stack and the BoP was investigated through the effect of recycling depleted fuel. The results showed that anode gas recycling could be used for managing the gradients within the stack, while also improving fuel utilisation and water management. Copyright (C) 2015, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.