Delivery of rapamycin loaded on core-multishell nanocarriers with different architectures supporting redox-induced drug release is investigated on human skin ex vivo by scanning transmission X-ray microscopy (STXM) near the O 1s-absorption edge (520–565 eV). The local concentration of the drug and nanocarriers in skin sections is obtained from linear combination modeling using reference spectra of the drug, nanocarriers, and untreated skin. This allows us to probe selectively rapamycin and nanocarriers as a function of exposure time reaching up to 5 days. Additionally, skin samples were treated with dibenzoyl peroxide (DBPO) to induce oxidative stress and simulate the local redox environment found in skin inflammatory conditions. It is shown that rapamycin and nanocarriers have different penetration profiles, which shed light on the drug transport and release mechanisms. These results make use of high spatial resolution at full chemical selectivity reaching down to 75 nm and are compared to skin penetration of topically applied rapamycin in different formulations. They highlight unique capabilities and the future potential of drug transport by polymeric drug nanocarriers.