The chemical composition, toxicity and biochemical efficacy of the Phyllanthus fraternus against three major stored grain pests was studied in the present study. The GC-MS revealed 4-Methoxy-1,3-butanediol, 2,4,6-trimethyloctane, 2,6-diisopropylnaphthalene, 2-pentadecanone, 6,10,14-trimethyl, methyl palmitate, and stearic acid were found to be major components of the active fraction from ethyl acetate extract of P. fraternus. In fumigant bioassay, it was proved that adults of stored grain insect pest are susceptible to active fraction and also showed potent grain protectant properties. Further, active fractions inhibited acetylcholinesterase enzyme activity in Sitophilus oryzae. In addition, a significant impairment in the antioxidative defense system, superoxide dismutase (SOD), catalase (CAT), reduced glutathione (GSH), glutathione peroxidase (GPx) and glutathione-S-transferase (GST) in test insects were observed. The results indicate that the toxicity of active fraction might be associated with inhibition of AChE activity and oxidative imbalance. In view of the strong fumigant toxicity of active fraction from P. fraternus extract as desirable tools for stored food grains against major stored grain pests and promoting eco-friendly pest control strategies.