Four stilbenoids and three anthraquinones isolated from the roots of Rheum palmatum L. were evaluated in their β-site amyloid precursor protein cleaving enzyme 1 (BACE1) inhibitory activity, targeting reduction of β-amyloid aggregation in the brain of Alzheimer’s disease (AD) patient. Among the compounds tested, two stilbenoids, rhapontigenin and desoxyrhapontigenin, showed potent BACE1 inhibitory activity with IC₅₀ values of 0.256 ± 0.008 and 2.028 ± 0.108 µM, respectively. In kinetic analysis, rhapontigenin was a mixed inhibitor of BACE1 with an inhibition constant K_ivalue of 0.28 ± 0.07 µM. Based on the secondary plots, K_I, a dissociation constant with the free enzyme, and K_IS, a dissociation constant for enzyme-substrate complex, of rhapontigenin were 0.29 ± 0.04 and 0.69 ± 0.15 μM, respectively, indicating the inhibition of rhapontigenin against BACE1 is type I. The docking analysis predicted that rhapontigenin had a high binding affinity by interacting with TYR132 and THR133 of BACE1 via hydrophobic interaction and hydrogen bonding, respectively. These results suggest that these stilbenoids exhibit high BACE1 inhibitory activity, and that rhapontigenin could be a candidate agent for the treatment of AD.