The skin is an effective barrier that prevents the influx of harmful substances from the environment and the efflux of body fluid. This barrier function is ascribed to the intercellular lipids present in the outermost layer of the skin referred to as the stratum corneum (SC). These lipids are composed mainly of ceramides (CERs), cholesterol, and free fatty acids (FFAs). Alterations in the SC lipid composition and barrier function impairment occur in several skin diseases including atopic dermatitis (AD). As the etiology of AD is multifactorial, establishing the relationship between the changes in SC lipid composition and barrier function impairment in the patients remains a challenge. Here, we employed model membrane systems to investigate the contribution of various anomalies in the SC CER and FFA composition observed in AD patients' skin to the barrier dysfunction. Using ethyl-p-aminobenzoate permeation and transepidermal water loss values as markers for barrier function, we determined that the alterations in SC lipid composition contribute to the impaired barrier function in AD patients. By the use of biophysical techniques, we established that the largest reduction in barrier capability was observed in the model with an increased fraction of short -chain FFAs, evident by the decrease in chain packing density. Modulations in the CER subclass composition impacted the lamellar organization while having a smaller effect on the barrier function. These findings provide evidence that AD therapies normalizing the FFA composition are at least as important as normalizing CER composition.