Atopic dermatitis (AD) is a chronic inflammatory skin condition that affects mostly young infants. The purpose of this research was to achieve a prolonged drug release and the reduction of side effects with hydrocortisone-loaded nanoparticles (NPs), for AD treatment. Poly(ε-caprolactone) (PCL) NPs were prepared by modified solvent displacement method and were characterized in terms of size, potential zeta, morphology, entrapment efficiency (EE), Fourier transform infrared (FT-IR) spectrometry and in vitro permeation studies using Franz cells. Toxicology of this nanosystem was also assessed. The obtained NPs EE showed an increased size and a more homogenous size distribution after loading and were negatively charged. EF was around 62%. In vitro release studies demonstrated a controlled release of drug from the NPs over time. FT-IR analysis showed the system stability for one week. Permeation studies revealed significant differences in the permeation of encapsulated and free hydrocortisone. In vitro toxicity studies showed no effect of drug toxicity after encapsulation. The study seems to indicate that encapsulation of hydrocortisone in PCL NPs could enable a faster control of the disease and a decrease in the side effects associated to the long-term application of corticosteroids.