Mupirocin is an antibacterial agent that has been documented to be effective in treating superficial skin infections. However, the main limitation of its application is bacterial resistance. Therefore, there is a need to determine a way to potentiate its efficiency. Accordingly, this obstacle led to this current investigation, which aims to find a way to improve the therapeutic action of mupirocin. This study focuses on the integration of tea tree oil with mupirocin to improve its antibacterial and wound healing capacities. Distinct nanoemulsions (NEs) were developed and the best of them were optimized using a central composite design (CCD) approach. The optimized NEs were mixed with a gel base to form a mupirocin-loaded nanoemulgel (NEG). The formulation was evaluated for characteristics including pH, viscosity, spreadability, and in vitro release over 6 h. The NEG was examined for its stability in two different conditions, namely at room temperature and refrigerated, for 3 months. Eventually, the NEG was inspected to determine its antibacterial and wound healing efficiencies. The developed mupirocin-loaded NEG exhibited good physical properties in terms of pH (6.13), viscosity (19,990 cP), spreadability (48.8 mm), and in vitro release over 6 h (51.4%). Moreover, it showed good stability with no significant difference in the evaluated parameters when stored for 3 months in the two conditions. Ultimately, mupirocin-loaded NEG prepared with tea tree oil exhibited a significant antibacterial influence in addition to good healing efficiency.