The aim of this study was to improve design of microtubular Solid Oxide Fuel Cell (mSOFC) stacks. Three-dimensional models were developed in order to investigate the effect of flow channel and fuel cells arrangement on thermal stresses of the mSOFC stacks and their performance. Two geometries of the anode-supported mSOFC stack were considered. The paper presents modifications of fuel cell arrangement in the stacks and analyses for two ways of stack cooling carried out by coupling a Computational Fluid Dynamics (CFD) and Computational Structural Mechanics (CSM). The simulation results indicate that the lowest value of the total displacement of the assembly was noticed for the mSOFC stack design with an external air flow cooling (case H-E). In addition, the smallest axial and total stresses were recognized for the same case H-E due to uniform temperature distribution, which limits strain of the materials and prevents development of excessive thermal stresses in the mSOFC stack components. Copyright (C) 2015, The Authors. Published by Elsevier Ltd on behalf of Hydrogen Energy Publications, LLC.