Background/Objectives: Breast cancer remains one of the leading causes of cancer-related mortality. Still, limited drug delivery systems for genistein, a powerful natural anticancer agent, draw significant attention. We aimed to develop a co-therapeutic/synergistic dual-compartment system; genistein-loaded pumpkisome nanovesicles (GNS-PKs) incorporated into pullulan microneedle patches (MNs), and to explore its anticancer activity. Methods: GNS-PKs were prepared and characterized for particle size (P.S), polydispersity (PDI), zeta potential (Z.P), encapsulation efficiency (E.E%), and stability. Afterward, they were embedded in pullulan-dissolving microneedle arrays and characterized for release kinetics, mechanical strength, and in vitro cytotoxicity. The in vivo efficacy was evaluated in mice with solid Ehrlich Ascites Carcinoma (EAC), focusing on tumor volume, oxidative stress, inflammatory cytokines, Epidermal Growth Factor (EGFR) expression biomarkers, and histopathological analysis. Results: The optimized nanovesicles had a particle size of 170 nm, a zeta potential of −42 mV, and an entrapment efficiency of up to 92%. Pullulan microneedles demonstrated significantly high mechanical strength and effective deep penetration. In addition to, it markedly decreased MCF-7 cellular viability (IC50 = 3.5 µg/mL). Besides, it had a 76% reduction in tumor volume, significantly increased the antioxidant activity (SOD, CAT, GSH), decreased the levels of inflammatory biomarkers (IL-6, COX-2, NF-κB), and markedly downregulated the EGFR expression (p < 0.0001). Histological study revealed decreased mitotic activity and large tumor cells, with minimal systemic damage. Conclusions: GNS-PKs-pullulan microneedle system offers a hope for an innovative, potent, effective, and non-invasive strategy for breast cancer treatment with high antitumor efficacy.