Pyraclostrobin, a new group of fungicide, was evaluated on its efficacy to suppress G. boninense as well as its effect on oil palm physiology, growth promotion, and induction of defense-related gene, β-1,3-glucanase. Hexaconazole was also used as a positive control. In vitro, the best inhibitory result was achieved using pyraclostrobin at 0.75 μg a.i. ml-1 with percentage inhibition of radial growth (PIRG) of 80%, followed by pyraclostrobin at 0.50 μg a.i. ml-1 (PIRG 73%) and hexaconazole at 0.15 μg a.i. ml-1 (PIRG 73%). Probit analysis also indicated that emulsifiable concentrate (EC) values of pyraclostrobin towards G. boninense mycelial growth were 0.25 μg a.i. ml-1 for EC50 and 0.58 μg a.i. ml-1 for EC75, which were further tested in vivo. In general, in vivo results indicated that the oil palm seedlings treated with pyraclostrobin at EC75 had significantly lower basal stem rot (BSR) infection, higher plant growth, and positive effects on plant physiology compared to pyraclostrobin at EC50 and were comparable to hexaconazole. Moreover, gene expression of β-1,3-glucanase in the seedlings treated with pyraclostrobin at EC75 indicated the highest level at the early stage. These results suggest that pyraclostrobin at EC75 was able to suppress BSR with high efficacy and significantly improved plant growth.