Gas flow in catalyst layer is important as it is the place where the electrochemical reactions take place. But it is challenging because the size of the pores is less than one micron and gas flow in the catalyst layer is no longer continuum, the Knudsen number cannot be neglected. As a result, the wall-gas collision must be re-considered, meaning that in the macroscopic models, the absolute permeability of the catalyst layer for different gases varies. To investigate this, we will simplify the pore geometry in catalyst layer into a bundle of tubes whose diameters can be derived from the pore-size distribution of the 3D (focused ion beam) FIB images. A model for gas flow in each tube is then simulated, the flow rate in the small pores have high resistance than big one, large difference start after pore size bigger than 100 nm. Use the pore volume percentage with different pore size diameter and porosity, we have calculate the average cross section area of the catalyst layer and calculate the average flow rate based on them which is used for the permeability calculation later. This permeability value can reflect the permeability in the true catalyst. The results show that permeability of catalyst layer is not a constant but varies with Knudsen number, meaning that the permeability calculation in the micro/nano scale is depend on the Knudsen number. Assuming a constant permeability for all the gases, as used in the available fuel cell models in literature, could give rise to significant errors. (C) 2015 Elsevier Ltd. All rights reserved.