Ganoderma boninense is the causal agent of basal stem rot (BSR) disease affecting oil palm in Southeast Asian countries. Previous reports have indicated the successful used of Scyralidium parasiticum (Sp) as biological control agent (BCA) against G. boninense. In this study, we screened 30 fractions obtained from Sp against G. boninense and characterized the possible compounds found in the fractions using liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF-MS). Three fractions were identified giving the best inhibition on the growth of the pathogen. Multivariate analysis indicated that the metabolite profiles of the three fractions were different substantially. Putative identification of the fractions led to number of potential compounds with antifungal role. Overall, the finding indicates that Sp has potential as antifungal agent against G. boninense and could be exploited in the management of G. boninense infection.