Drug vectorization to hair follicles favors skin drug penetration, contributing to the optimization of treatment of diseases as alopecia areata (AA). In this context, this work aimed to develop and characterize nano-sized minoxidil (MXD) formulations to sustained and target drug delivery to hair follicles for the optimization of AA treatment. Nanoemulsions were prepared by ultrasonication. The influence of 3 independent variables at 2 levels and 3 replicates of center point was evaluated, totalizing 11 experimental runs. Three optimized nanoemulsions were studied (NE 5, NE 6 and NE 8). Clove oil and Kolliphor® P188 were selected as oil phase and surfactant, respectively. Optimized nanoemulsions showed monomodal size distributions, mean droplet size of 10 nm with PdI smaller than 0,2 and stability against coalescence at room temperature and relative humidity levels around 50%. Nanoemulsions controlled drug release 2 times more effectively than control sample for at least 6 h, with the predominance of Higuchi release kinetic model. MXD skin penetration from nanoemulsions was raised by more than 9 times, compared with conventional ethanol-based solutions. Follicular drug penetration experiments showed that nanoemulsions containing MXD penetrated into hair follicles more than 26 times more efficiently than control sample, suggesting that the proposed clove oil-based nanoemulsions constitute a promising approach for the topical treatment of alopecia.