Extensively drug-resistant (XDR) bacteria pose a serious global public health threat due to their high levels of resistance to multiple classes of antibiotics. This study aimed to characterize bacterial isolates obtained from clinical samples, evaluate their antibiotic resistance patterns, and investigate the antimicrobial and anticancer potential of essential oils (EOs) and their nanoemulsions (NEs). A total of 175 bacterial isolates were collected from various clinical sources, identified, and subjected to antibiotic susceptibility testing using both conventional methods and the VITEK^® 2 system. Among these, nine isolates were identified as extensively drug-resistant. Among the tested EOs, carvacrol exhibited the strongest antibacterial activity, with minimum inhibitory concentrations (MICs) ranging from 14 to 35 µg/mL, compared to 8 to 19 µg/mL for meropenem. To enhance its stability and efficacy, carvacrol nanoemulsions (CANE) were prepared via ultrasonication and characterized using zeta potential measurements, which indicated a positive surface charge of +14.2 mV, while dynamic light scattering (DLS) analysis revealed a narrow size distribution with a mean hydrodynamic diameter of 411.3 nm. High-resolution transmission electron microscopy (HR-TEM) showed spherical droplets ranging from 18 to 144 nm in size, with an average diameter of 69 ± 28 nm. The nanoemulsion formulation significantly enhanced antibacterial activity, with MICs reduced to 11 ± 0.0–23 ± 0.21 µg/mL, compared to 14 ± 0.13–35 ± 0.11 µg/mL for pure carvacrol oil. Gas chromatography–mass spectrometry (GC–MS) analysis identified major active constituents, including thymol, methoxyphenyl, estragole, and D-limonene, which are likely contributors to the observed antimicrobial and anticancer effects. In addition, carvacrol nanoemulsions demonstrated potent cytotoxicity against multiple human cancer cell lines (HepG2, MCF-7, PC-3, and Caco-2) while showing minimal toxicity toward normal cells. Confocal microscopy further confirmed apoptosis induction in treated cancer cells, suggesting a mitochondria-mediated apoptotic pathway. In conclusion, this study highlights the strong therapeutic potential of essential oils—particularly carvacrol and its nanoemulsion formulation—as dual-action agents exhibiting broad-spectrum antibacterial activity against XDR pathogens and selective cytotoxicity against cancer cells.