Stratum corneum (SC), the outer layer of skin, serves as a barrier for pathogens and maintains the trans-epidermal water loss. The lipid matrix of SC is the major diffusion-rate-limiting pathway as molecules will have to pass through it. Ceramides play a key role in structuring and maintaining the barrier function of the skin. In this study, atomistic molecular dynamics (MD) simulations were used to systematically investigate the effects of the chain length of ceramide (CER) tails on the properties of the bilayer at a skin temperature of 310 K. The barrier properties were examined by means of permeation studies of water through the model membrane using steered MD simulations. Our studies revealed that shorter chains of one leaflet of the bilayer do not interdigitate with the chains of the other leaflet and lead to more free space in the middle of the bilayer, thereby leading to higher permeability. In CERs with dissimilar chain lengths, the lipids on one chain interdigitate with the other leaflet lipids, increasing the electron density in the middle of the bilayer. The bilayer thickness increases with increase in the CER chain length. The permeability of smaller-chain CERs was found to be an order of magnitude higher than that of the longer-chain CERs.