Aspergillus nidulans, an endophytic fungus isolated from the medicinal plant Acacia nilotica showed potent antifungal activity against oral pathogenic strains of Candida albicans. Biofilm forming C. albicans was isolated and tested for its susceptibility to various solvent extracts of A. nidulans using biofilm inhibition assay. Gas chromatography-mass spectrometry (GC-MS) analysis was performed to identify the potential compounds in the endophytic fungal extract and mode of interaction of these compounds with the target enzyme of C. albicans was revealed using molecular docking analysis. All the solvent extracts showed good inhibitory activity on the biofilm forming C. albicans strain with maximum activity in the chloroform extract. The percentage reduction in biofilm inhibition for chloroform, ethyl acetate, hexane and methanol extracts were 74.86%, 72.53%, 60.61% and 52.60% respectively. GC-MS analysis of chloroform extract revealed the presence of flavonoids, fatty acids, amides etc. of which the flavonoids-saltillin, taxifolin and 6-methoxyflavone showed good binding interaction with the C. albicans growth regulator N-myristoyltransferase (NMT). The bioactive compounds present in A. nidulans not only inhibit C. albicans growth but also controls the biofilm formation thereby reducing the virulence of C. albicans.