Problem: Endometriosis (EMs) is characterized by the presence of endometrial stroma and glands outside the uterus. Our previous study showed that baicalein inhibited proliferation and induced apoptosis in EMs. However, the effects of baicalein on the invasiveness of ectopic endometrial stromal cells (EcESCs) remain unclear. The aim of this study was to assess the potential anti-invasive effect of baicalein and determine the underlying mechanism. Methods: The invasive and migratory properties of EcESCs were assessed in vitro using Transwell and wound healing assays. The expression of functional markers of EcESCs, including matrix metalloproteases (MMPs), FURIN, and TGFB1, was analyzed using WB and ELISA. Additionally, a mouse model of EMs was treated with baicalein (10 mg/kg/d and 35 mg/kg/d) for 4 weeks. The weight and number of ectopic lesions were determined, and the expression of markers was assessed using immunohistochemistry. Results: Baicalein inhibited the invasion of EcESCs and the expression of certain invasion-related proteins, including MMP9, MMP2, and MT1-MMP. Exposure to baicalein reduced the extracellular levels of TGFB1 in EcESCs and the reduced expression of TGFB1, resulting in decreased expression of FURIN in EcESCs, which serves a pivotal role in the transformation of pro-MT1-MMP to activated MT1-MMP. In the mouse model of EMs, intraperitoneal injection of baicalein inhibited the growth of ectopic lesions and reduced MT1-MMP, FURIN, and TGFB1 expression. Conclusions: Baicalein reduced the invasion of EMs, potentially by restricting the FURIN-MT1-MMP-mediated cell invasion of EcESCs maybe through reduction of the autocrine of TGFB1.