The aim of this work was to investigate the skin penetration enhancer effect of a sucrose ester (SE) in an Ibuprofen (IBU) containing hydrogel and to examine its influence on the special lipid bilayer of the stratum corneum (SC). ATR-FTIR spectroscopic measurements were performed combined with tape stripping method on hairless mice in vivo. A SE containing gel was compared to another gel without SE. It was found that the preparations caused only minimal modifications in the lipid and the protein structure, promoting the skin hydration and therefore also the penetration of IBU. Although the degree of moisturization and penetration were more intense in the case of the SE containing gel treatment, it did not cause greater alterations in the SC structure than the gel without SE. It has been proven that SE acts as an effective and non-irritating hydration and penetration enhancer for IBU through skin.