The study aims to evaluate the neuroprotective properties of Pterocarpus marsupium Roxb. The bioactive optimized hydroalcohol-extracted fractions of bark (PMBHA) and heartwood (PMHHA) at 300 and 400 mg/kg were examined in rats with scopolamine-induced neurotoxicity to study oxidative, neurochemical, and neuroinflammation biomarkers. Phenol and flavonoid-rich radical scavengers in contributing total antioxidant capacities of PMBHA and PMHHA quenched peroxyl radicals and protected the cellular membrane and lipoproteins from ROS in DPPH, ORAC, and CAP-e tests. In anticholinesterase activities, PMBHA inhibited AChE (IC50: 54.40 ± 0.98 µg/mL) and BChE (IC50: 50.95 ± 0.98 µg/mL) mixed-competitively, while PMHHA inhibited cholinesterase activities (AChE: 42.23 ± 0.54, and BChE: 47.19 ± 0.65 µg/mL) competitively. Dosage at 300 and 400 mg/kg of PMBHA and PMHHA improved serum and brain oxidative indicators (MDA, SOD, CAT, and GSH), and restored proinflammatory cytokines (TNF-α, and IL-6) leading to enhanced brain cholinesterase and β-secretase levels in neurotoxic rats. GC-MS reported antioxidant, anti-inflammatory, and neuroprotective compounds of PMBHA catechol, thiamet-G, d-Gala-l-ido-octonic amide, falcarinol, D-mannose, ribitol, 1,2,4-cyclopentanetrione, 3-(2-pentenyl)-, hexadecanoic acid methyl ester, n-hexadecanoic acid, oleic acid, and 3,5-Dimethoxybenzyl alcohol, α-epi-7-epi-5-Eudesmol, 1 R,4aR,7 R,8aR)-7-(2-Hydroxypropan-2-yl)-1,4a-dimethyldecahydro naphthalen-1-ol, arctiol, 1,1,4,7-tetramethyldecahydro-1 H-cyclopropa[e]azulene-4,7-diol, 2-Propen-1-ol, 3-(2,6,6-trimethyl-1-cyclohexen-1-yl), 4-t-Butyl-2-[4-nitrophenyl]phenol in PMHHA were responsible in neuroprotection in neurotoxic rats. However, heartwood demonstrated better neuroprotective activities than the bark of P. marsupium due to some of the key compounds (1 R,4aR,7 R,8aR)-7-(2-Hydroxypropan-2-yl)-1,4a-dimethyldecahydronaphthalen-1-ol, 2-Propen-1-ol, 3-(2,6,6-trimethyl-1-cyclohexen-1-yl)-, 4-t-Butyl-2-[4-nitrophenyl]phenol, 1,1,4,7-Tetramethyldecahydro-1 H-cyclopropa[e]azulene-4,7-diol.