Sinomenine is an alkaloid derived from Chinese medicinal plant Sinomenium acutum. Our previous studies suggested that sinomenine can inhibit the metastasis of breast cancer. However, whether sinomenine can inhibit the metastasis characteristics of breast cancer side population (SP) cells is still unknown. In present study, we isolated the side population (SP) cells from MDA-MB-231 cells by fluorescence-activated cell sorting (FACS). MDA-MB-231 SP cells were treated with different concentrations of sinomenine at the absence or presence of hypoxia, and cell viability were measured by CCK-8 assay. The transwell invasive assay were conducted to assess of the effect of sinomenine on the invasion of hypoxic MDA-MB-231 SP cells. The protein expression was detected by Western blot assay. Sinomenine inhibited the cell viability and invasion of hypoxic MDA-MB-231 SP cells. Western blot assay results showed that the upregulation of MMP-2 and MMP-9 by hypoxia was inversed by sinomenine. Additionally, it was found that sinomenine suppressed the activation of PI3K/Akt/mTOR pathway under hypoxia in MDA-MB-231 SP cells. Moreover, the inhibiton of sinomenine on metastasis of hypoxic MDA-MB-231SP cells and PI3K/Akt/mTOR pathway could be rescued by PI3K activator IGF-1. Our study suggested that sinomenine inhibits invasion of breast cancer SP cells under hypoxia through PI3K/Akt/mTOR pathway.