Background Vancomycin (VCM)-induced hepatotoxicity is a significant clinical concern due to its association with oxidative stress, apoptosis, and inflammatory responses. This study investigated the formulation and potential preclinical application of rutin-loaded nanocapsules (RUT-NC) as a hepatoprotective agent against VCM-induced liver injury. Methods Hepatotoxicity was induced in rats through VCM administration, followed by oral treatment with RUT-NC. Liver function, oxidative stress markers, apoptotic proteins, lipid metabolism regulators, and inflammatory cytokines were subsequently evaluated. Results RUT-NC treatment significantly improved liver function parameters, attenuated oxidative stress, and modulated apoptotic pathways by downregulating the expression of p38, p53, caspase-8, miR-122, miR-7, and beclin-1. Furthermore, RUT-NC restored lipid metabolism homeostasis by regulating the expression of PPAR-α, FASN, and SREBP-1. Notably, it exerted potent anti-inflammatory effects by suppressing NF-κB, TNF-α, IL-1β, IL-6, IL-17, and Gasdermin-D, thereby mitigating chronic liver inflammation. The pathological effects of VCM administration on hepatocytes were effectively counteracted by RUT-NC. Conclusion RUT-NC demonstrates promising hepatoprotective properties by enhancing antioxidant defenses, inhibiting apoptosis, regulating lipid metabolism, and reducing inflammation. These findings highlight its potential as a therapeutic intervention for drug-induced liver injury (DILI) and warrant further investigation for clinical application.