Sophora pachycarpa Schrenk ex C.A.Mey. is an annual plant belonging to the family Fabaceae. The cytotoxic activities of methanol-dichloromethane extracts (1:1) of different parts of S. pachycarpa were investigated on DU145 (prostate cancer cell line) and MCF-7 (breast cancer cell line) cell lines. The root extract of S. pachycarpa was the only extract that showed significant cytotoxic activity with IC50 values of 39.88 and 16.49 μg/mL on DU145 and MCF-7 cell lines, respectively. The root extract was then subjected to RP-HPLC for further fractionations. Among the isolated fractions from root extract, only one of them had remarkable cytotoxic effects with IC50 value of 26.43 on MCF-7 and 7.54 μg/mL on DU145 cell lines. Further purification led to isolation of a compound with IC50 values of 5.44 and 2.44 μg/mL on MCF-7 and DU145 cell lines, respectively. Based on 1H NMR and 13C NMR spectra, together with LC-MS, the structure of the purified compound was assigned as the flavonostilbene alopecurone A.