Confocal Raman microscopy has a number of advantages in investigating the human stratum corneum (SC) in vivo and ex vivo. The penetration profiles of xenobiotics in the SC, as well as depth profiles of the physiological parameters of the SC, such as the concentration of water depending on the strength of hydrogen bonds, total water concentration, the hydrogen bonding state of water molecules, concentration of intercellular lipids, the lamellar and lateral packing order of intercellular lipids, the concentration of natural moisturizing factor molecules, carotenoids, and the secondary and tertiary structure properties of keratin are well investigated. To consider the depth-dependent Raman signal attenuation, in most cases a normalization procedure is needed, which uses the main SC’s protein keratin-related Raman peaks, based on the assumption that keratin is homogeneously distributed in the SC. We found that this assumption is not accurate for the bottom part of the SC, where the water concentration is considerably increased, thus, reducing the presence of keratin. Our results demonstrate that the bottom part of the SC depth profile should be multiplied by 0.94 in average in order to match this non-homogeneity, which result in a decrease of the uncorrected values in these depths. The correctly normalized depth profiles of the concentration of lipids, water, natural moisturizing factor and carotenoids are presented in this work. The obtained results should be taken into consideration in future skin research using confocal Raman microscopy.