Basal Stem Rot (BSR) caused by Ganoderma boninense poses a threat to the sustainability of oil palm (Elaeis guineensis Jacq.), a valuable export commodity in Southeast Asia. This study focuses on evaluating the potential of an indigenous strain of Fusarium, as a biocontrol agent for BSR. The research involves chemical characterisation and laboratory testing. Molecular identification confirmed the isolate as Fusarium foetens, an unconventional biocontrol agent that showed promising results in experimental settings. In the disc vapour assay, discs containing volatile organic compounds (VOCs) effectively inhibited the growth of G. boninense by up to 60%. Analysis of scanning electron microscopy (SEM) imagery suggested that the inhibition might be attributed to cell wall damage and internal disruption caused by the VOCs. Four major VOCs were identified and ranked based on their relative peak area (%), including 2,3-Pyrazinedicarboximide (15.54%), 2-(2-Butoxyethoxy) ethyl thiocyanate (11.43%), 3,5-Dimethoxyphenol (11.40%), and Indolylmethylthiohydroximate (5.56%), with other minor compounds accounting for less than 5.00%. Docking simulations using PyRx software were performed to analyse the binding affinity between selected VOCs and the virulent protein, xyloglucan-specific endo-beta-1,4-glucanase (XEG). Interestingly, two compounds, 2,3-Pyrazinedicarboximide and indolylmethylthiohydroximate, had exhibited binding affinities similar to that of hexaconazole, a standard antifungal agent used in BSR management.