Caesalpinia bonducella, known as ‘tombili’ belongs to the family of Fabaceae. Tombili has been empirically used as traditional medicine. In a previous study, phytochemical screening showed that tombili seed contained alkaloid, flavonoid, terpenoid, and tannin compounds. This research aimed to isolate an antioxidant compound from tombili seed extract. Fractionated using n-hexane, ethyl acetate, and methanol as a solvent. All fractions were tested for their antioxidant potential. The ethyl acetate fraction gave a better antioxidant potential (IC50 86.153±4.22 ppm) than it has purified. Characterization of an isolated compound using various spectroscopies data, including UV, FTIR, 1D-NMR, 2D-NMR, and LCMS/MS. The structure of the isolated compound was suggested as 7- (β-DGlucopyranosyloxy) 5-hydroxy-2-(4-hydroxyphenyl)-6-methoxy-4H-1-benzopyran-4-one (homoplantaginin). The IC50 value of the isolated compound was 40.53 ±3.13 ppm, indicating the isolated compound has potent antioxidant activity.