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Antifungal drug resistance in filamentous fungi, particularly <i>Aspergillus</i> species, is increasing worldwide. Therefore, new antifungal drugs or combinations of drugs are urgently required to overcome this public health situation. In the present study, we examined the antifungal activity of vancomycin-functionalized AuNPs. These functionalized AuNPs were characterized, and their antifungal activity and associated killing mechanism were investigated using conventional methodologies against the conidia of <i>A. fumigatus</i> and <i>A. flavus</i>. The differential antifungal activity of vancomycin-functionalized Au-NPs against the conidia of <i>Aspergillus</i> species is dependent on structural differences in the conidial cell wall. The results demonstrated potent fungicidal activity against <i>A. fumigatus</i>, with a MIC value of 4.68 µg/mL, 93% germination inhibition, and 38.4% killing rate within 8 h of exposure. However, the activity against <i>A. flavus</i> was fungistatic; a MIC value of 18.7 µg/mL and 35% conidial germination inhibition, followed by 28.4% killing rate, were noted under similar conditions. Furthermore, endogenous reactive oxygen species (ROS) accumulation was 37.4 and 23.1% in conidial populations of <i>A. fumigatus</i> and <i>A. flavus</i>, respectively. Raman spectroscopy analysis confirmed the possible (but not confirmed) binding of functionalized AuNPs with the chitin and galactomannan components of the cell wall. A potential strategy that involves the exploration of antibacterial drugs using AuNPs as efficient drug carriers may also be appropriate for countering emerging drug resistance in filamentous fungi.