Endometriosis (EM) is a common benign gynecological disease with complex pathogenesis and lack of unified understanding. In recent years, the theory of stem/progenitor cells has gradually been recognized by scholars. The presence of stem/progenitor cells in the endometrium and researchers’ understanding of stem/progenitor cell specific markers has been further developed, which is of great significance for sorting stem/progenitor cells and further elucidating their roles in the pathogenesis of EM. At present, more endometrial stem cell signaling pathways have been studied including Wnt, Hedgehog, Notch, phosphatidylinositol-3-kinase/protein kinase B, Smad/connective tissue growth factor, CXCL12/CXCR4, etc. These signaling pathways can regulate stem cell involvement in the pathogenesis of EM. Exploring how signaling pathways to regulate stem cell involvement in the pathogenesis of EM can help elucidate the specific pathogenesis of EM and provide new directions for its treatment. This paper will summarize them.