Infectious diseases constitute a problem of great importance for animal and human health, as well as the increasing bacterial resistance to antibiotics. In this context, medicinal plants emerge as an effective alternative to replace the use antibiotics. The essential oil (EO) of Minthostachys verticillata (Griseb.) Epling (Lamiaceae) has demonstrated a strong antimicrobial activity. However, its instability and hydrophobicity under normal storage conditions are limitations to its use. Nanoemulsion technology is an excellent way to solubilize, microencapsulate, and protect this compound. This study aimed to obtain a nanoemulsion based on M. verticillata EO and evaluate its antibacterial activity against Staphylococcus aureus. The EO was obtained by steam distillation. Identification and quantification of their components were determined by GC-MS revealing that the dominated chemical group was oxygenated monoterpenes. Nanoemulsions (NE) were characterized by measuring pH, transmittance, separation percentage, release profile, and morphology. The effect of NE on the growth of S. aureus and cyto-compatibility was also evaluated. The results showed that NE containing a higher percentage of tween 20 exhibited higher stability with an approximated droplet size of 10 nm. The effect of encapsulation process was evaluated by GC-MS revealing that the volatile components in EO were no affected. After 24 h, 74.24 ± 0.75% of EO was released from NE and the antibacterial activity of EO was enhanced considerably by its encapsulation. The incubation of S. aureus with the NE and pure EO, show a bacterial growth inhibition of 58.87% ± 0.99 and 46.72% ± 3.32 (p < 0.05), respectively. In addition, nanoemulsión did not cause toxicity to porcine and equine red blood cells. The results obtained showed that NE could be a potential vehicle for M. verticillata EO with promissory properties to emerge as a tool for developing advanced therapies to control and combat infections.