In the second part of this study, a new analytical model for catalyst layers (CLs) compression is developed using effective medium theory, using a geometric "unit cell", to accurately predict the deformation of CLs under compression. Based on SEM images, a representative unit cell is proposed using microstructural properties of CL such as porosity, pore size distribution, and ionomer to carbon weight ratio (I/C) to simplify the random complex structure of CLs. Deformation of the ionomer film that covers carbon agglomerates is found to be the main deformation compared to other mechanisms such as Hertzian compliance of carbon particles and deformation of agglomerates. The present model is validated using the experimental results obtained for five different CL designs, presented in Part 1 of this study. The analytical model is capable of predicting the non-linear compressive behaviour of CLs with a reasonable accuracy since a continuous change of CL porosity is considered in the model. The proposed geometrical model has also been used for other properties of CL in our group and successfully predicted thermal conductivity and gas diffusivity of CL. (C) 2019 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.