Endometriosis (EMs) is a prevalent benign gynecological condition known for exhibiting malignant-like biological activities, including the migration and proliferation of endometrial stromal cells (ESCs). Hydroxysafflor yellow A (HSYA), the principal active component derived from safflower yellow, possesses notable anti-proliferative and anti-migratory effects. This study explored the potential therapeutic efficacy of HSYA and elucidated its underlying mechanisms in experimental EMs models. Results from CCK-8 assays, EdU staining, and wound healing assays demonstrated that HSYA significantly reduced ESC viability, proliferation, migration, and invasive capabilities in a concentration-dependent manner. Additionally, HSYA decreased protein expression of proliferating cell nuclear antigen (PCNA), N-cadherin, and vimentin, while enhancing levels of cleaved caspase-3 (CC3), markers integral to EMs progression. Mechanistically, HSYA activated the PPAR-γ/PTEN/Akt signaling pathway in ESCs, evidenced by increased expression of PPAR-γ and PTEN along with reduced Akt activity. Importantly, silencing PPAR-γ expression diminished HSYA-mediated effects on ESC biological behavior. Consistent with in vitro findings, HSYA treatment in vivo effectively inhibited growth of endometriotic lesions, exhibiting anti-proliferative, anti-migratory, anti-invasive, and pro-apoptotic properties. Collectively, these data suggest HSYA as a promising candidate for EMs therapy.