We evaluated the ability of hydroxypropyl-β-cyclodextrin (HPβCD) to influence the percutaneous absorption of capsaicin (CP) through isolated rat skin. Phase solubility analysis and phase distribution studies suggested the potential of HPβCD as a solubilizer and permeation enhancer for CP. In vitro permeation studies showed the trend that, the penetration flux (Js) of CP increased with the increasing concentration of HPβCD from 0 to 2.20% (w/v), and then decreased dramatically when the concentration of HPβCD kept on increasing up to 15% (w/v). 2.20% (w/v) of HPβCD provided both just adequate solubilization and preferred Js for the permeation of CP (0.075%, w/v). Similar change patterns of the permeation parameters were also observed in the hydrogels, but the Js of CP was reduced significantly along with the increasing concentration of Carbopol U21. Histological analysis showed an invasive action of HPβCD on the stratum corneum (SC) of rat skin, which could only reduce the lag time (TL) but could not increase the Js of CP. On the other hand, the complexation of HPβCD with CP could attenuate this invasive action. It is inferred that excess of HPβCD could not only disturb the percutaneous absorption of CP but also disrupt the structure of SC.