A dynamic solid oxide fuel cell (SOFC) model is used to investigate the effects of different flow arrangements, as well as those of non-uniform air flow across channels, on temperature profile and thermal gradients under transient and steady state response. A high performance multi-input multi-output feedback controller has been developed to minimize SOFC spatial temperature variations during changes in power demands for different flow patterns. Numerical results show that the controller would result in negligible temperature variations for the modified cross-flow arrangement proposed here, even for large changes in the power drawn. The combination of a high performance controller and design modification results in a more uniform temperature profile at steady state nominal conditions, and modest variations in temperature profile, from the nominal, for +/- 15% change in power. Similarly, non-uniform air flow rate decreases the temperature gradient as well as maximum temperature across the cell, though its effect is less pronounced in the closed loop response. (C) 2016 Elsevier Ltd. All rights reserved.