Objective: Over expression of SIRT1, is implicated in many cancers and therefore could become a promising antitumor target. Here we demonstrate a small molecule inhibitor, with potent inhibitory effects on the proliferation of breast cancer stem cells. Materials and Methods: Breast cancer stem cells cultured in RPMI-1640 medium and treated with and without small molecule inhibitor. The percentage of apoptotic cells was measured by flow cytometry. Real-time quantitative RT-PCR was performed to quantitatively estimate the mRNA expression of Sirtuin1 at different times. Results: Our findings indicated that small molecule inhibitor could effectively induced apoptosis in breast cancer stem cells. Further we showed expression of SIRT1 was dramatically down-regulated by small molecule inhibitor treatment with asending time. Conclusion: Small molecule inhibitor as a single agent through decrease expression of Sirtuin1 gene induced significant apoptosis of breast cancer stem cells. So, the small molecule inhibitor may have constituted novel anticancer agent.