The skin acts as a physical barrier to protect the body from the external physical and chemical environment. When skin is infected, the outer epidermal barrier is compromised and colonized with microbial growth. Wound infection presents an immense burden on healthcare costs and decreased the quality of life for patients. The topical application of nanoemulsions (NE) at pathological sites offers the potential advantage of direct drug delivery to the skin including the potential for follicular targeting. This may have application in the improvement of skin antisepsis. In this study, NEs of triclosan (TSN) were prepared using hot high shear homogenization followed by ultrasonication. The oil phases comprised eucalyptus oil (EO) and olive oil (OO) and pseudo-ternary phase diagrams were used to select optimum concentrations of surfactant. EO-based NEs had smaller droplet sizes and higher entrapment efficiency compared to OO-based NEs. Skin permeation was higher for EO-containing formulations, likely due to the higher solubility of TSN in EO, smaller droplet size, low viscosity, and permeation enhancement effects of EO. Significantly, TSN was retained within the skin, demonstrating the potential of NEs for targeting hair follicular delivery within the skin, which may help improve the success of topical antisepsis.