Aspergillus flavus is a common human pathogen that releases mycotoxin into the host and is frequently treated with synthetic fungicides, but the fungicides have serious human health consequences. Natural products derived from higher plant species have long been investigated as a potential means of controlling pathogenic microorganisms. The indigenous vegetables Boesenbergia rotunda and Syzygium aromaticum are widely distributed in the tropical area. These plants have also been reported in traditional uses for the antimicrobial activity. The purpose of the study was to explore the antifungal susceptibility of dichloromethane and ethanol extracts of B. rotunda rhizomes and S. aromaticum flower buds by Soxhlet’s apparatus against A. flavus using the poison food technique. The effective extract was also subjected to preliminary phytochemical screening tests. The experiment used a completely randomized design with triplications. B. rotunda ethanol extract demonstrated significantly higher potential antifungal activity. The values of minimum inhibitory concentration (MIC) and minimum fungicidal concentration (MFC) of B. rotunda ethanol extract were 6.25 and 50 mg/ml, respectively, when tested using the macro-dilution method. According to phytochemical tests, the ethanol extract also contained alkaloids, flavonoids, cardiac glycosides, and saponins. The study suggests that a basic guideline for using this as an effective antifungal compound should be separated from the B. rotunda ethanol extract in the future for topical anti-pathogenic fungus.