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Nanomedicine holds great potential for drug delivery to achieve more effective and safer cancer treatment. Earlier, we reported that the alcoholic extract of Withania somnifera leaves (i-Extract) has selective cancer cell killing activity. Herein, we developed a folate receptor-targeting i-Extract nanocomplex (FRi-ExNC) that suspends well in water and possesses enhanced selective anticancer activity in both in vitro and in vivo assays. Comparative analyses of folate receptor (FR)-positive and -negative cells revealed that FRi-ExNC caused a stronger decrease in Cyclin D/Cdk4 and anti-apoptotic protein Bcl-2, as well as a higher increase in the growth arrest regulating protein p21WAF1 and pro-apoptotic protein PARP-1, in FR-enriched cancer cells. Our results demonstrate that FRi-ExNC could be a natural source-based nanomedicine for targeted cancer therapy.