Transcutaneous delivery attracts much attention but remains a challenging strategy for hydrophilic macromolecular drug administration. In the present study, we demonstrated that a solid-in-oil (S/O) nanodispersion, an oil-based nanodispersion of hydrophilic drugs, effectively enhanced the permeation of proteins into the skin. All of the different model proteins, FITC-labeled insulin (MW ca. 6 kDa), enhanced green fluorescent protein (EGFP, MW ca. 27 kDa) and horseradish peroxidase (HRP, MW ca. 40 kDa), permeated through the stratum corneum of Yucatan micropig skin in vitro by forming a S/O nanodispersion. The penetrated EGFP and HRP exhibited green fluorescence and catalytic activity, respectively, suggesting that these proteins can permeate into the skin in a functional form. The results indicated the potential utility of the S/O nanodispersion as a novel vehicle for transcutaneous protein delivery.