Ganoderma boninense is a fungal pathogen responsible for causing basal stem rot disease in oil palm. This study focuses on exploring the biocontrol potential of indigenous bacterium by detecting several bioactive compounds capable of inhibiting the growth of G. boninense. The 16S rRNA sequence analysis proved that the bacterium was Bacillus subtilis strain MN704394.1. The ethanolic extracts of bacterium culture supernatant, spanning 8 to 24 hr, were collected and tested on their inhibitory effects against G. boninense using simultaneous, preventive, and curative methods. The one obtained at the 8th hour using the preventive method demonstrated the highest inhibition percentage at 96.44%. By using GC-MS analysis, three compounds were consistently detected at all time points, which are eicosane, ethyl stearate and methyl palmitate. Eicosane and ethyl stearate were identified as bioactive compounds. Specifically, at the 8th hr, eicosane constituted 68.7467% of the total area, while ethyl stearate accounted for 10.3018%. Eicosane, a straight-chain alkane consisting of 20 carbon atoms, exhibited antifungal activity. Ethyl stearate, belonging to the group of fatty acid esters, demonstrates significant inhibitory activity against G. boninense. The potential of these two compounds is substantial, with prospects for further development, particularly in controlling G. boninense.