Polymeric micelles, which form through the self-assembly of poly(ethylene glycol)-poly(amino acid) block copolymers, are systemic nanocarriers in targeted cancer therapy. These micelles can encapsulate therapeutic compounds, such as lipophilic substances, charged compounds, and metal complexes, that have characteristics of increased solubility, sustained release, and improved tissue distribution. However, few studies have been conducted on the local distribution of polymeric micelles. Thus, we evaluated the skin penetration pattern of hydrophobic drugs in polymeric micelles. We revealed that improved water solubility by the encapsulation of the hydrophobic drugs indomethacin and resveratrol in polymeric micelles significantly increased the amount of drugs penetrating into the skin. Moreover, polymeric micelles did not enhance the permeability of drugs. Furthermore, although the polymers remained on or in the stratum corneum, the encapsulated drugs gradually moved deeper into the skin. These results indicate that encapsulated hydrophobic drugs in polymeric micelles can penetrate the living cell layer of the skin without bringing about unexpected side effects associated with other ingredients in the formulation. Thus, polymeric micelles for encapsulating hydrophobic drugs can be used for skin applications.