Endometriosis (EM) is a benign gynecological condition characterized by the aberrant proliferation of endometrial cells outside the uterine cavity. This pathological cell growth, accompanied by neoangiogenesis, contributes to the formation of EM lesions. Current pharmacological interventions for EM are often associated with adverse side effects, underscoring the necessity for alternative therapeutic strategies to improve disease management. Small interfering RNA (siRNA) therapeutics have emerged as a versatile pharmaceutical platform for treating a range of diseases; however, their clinical application is limited primarily by challenges related to effective delivery. Peptide-based nanoparticles designed for siRNA delivery offer a promising solution by enabling receptor-specific targeting and mitigating issues related to excessive positive charge. In this study, we engineered ternary polyplexes comprising anti-VEGFA siRNA, a cationic arginine-rich polymer, and an anionic glutamate-rich polymer functionalized with a cyclic RGD (cRGD) peptide to target αVβ3 integrins. These polyplexes were subjected to physicochemical characterization, and their cytotoxicity and gene silencing efficacy against a GFP reporter were evaluated in vitro. The anti-angiogenic potential of the formulations was further assessed in vivo using a surgically induced EM model in female Wistar rats. Treatment with cRGD-decorated, anti-VEGFA siRNA-loaded peptide-based nanoparticles resulted in a significant reduction in the volume of EM lesions, accompanied by decreased VEGFA mRNA expression and diminished surface expression of the endothelial marker CD34, relative to control nanoparticles lacking the targeting ligand. Collectively, these findings demonstrate that anionic nanoparticles targeting αVβ3 integrins can effectively suppress angiogenesis within EM lesions, highlighting their potential as promising candidates for the development of anti-angiogenic therapies in endometriosis.