The aim of this study was to evaluate the effect of vehicle and chemical modifications of the structure of active compounds on the skin permeation and accumulation of ibuprofen (IBU). As a result, semi-solid formulations in the form of an emulsion-based gel loaded with ibuprofen and its derivatives, such as sodium ibuprofenate (IBUNa) and L-phenylalanine ethyl ester ibuprofenate ([PheOEt][IBU]), were developed. The properties of the obtained formulations were examined, including density, refractive index, viscosity, and particle size distribution. The parameters of release and permeability through the pig skin of the active substances contained in the obtained semi-solid formulations were determined. The results indicate that an emulsion-based gel enhanced the skin penetration of IBU and its derivatives compared to two commercial preparations in the form of a gel and a cream. The average cumulative mass of IBU after a 24 h permeation test from an emulsion-based gel formulation through human skin was 1.6–4.0 times higher than for the commercial products. Ibuprofen derivatives were evaluated as chemical penetration enhancers. After 24 h of penetration, the cumulative mass was 1086.6 ± 245.8 for IBUNa and 948.6 ± 87.5 µg IBU/cm2for [PheOEt][IBU], respectively. This study demonstrates the perspective of the transdermal emulsion-based gel vehicle in conjunction with the modification of the drug as a potentially faster drug delivery system.