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Balanites aegyptiaca (B. aegyptiaca) is an African herb with traditional medical applications. Various pathogenic factors cause hepatic fibrosis and require novel treatment alternatives. Nanoformulation-based natural products can overcome the available drug problems by increasing the efficacy of natural products targeting disease markers. The current study investigated B. aegyptiaca methanolic extract using high-pressure liquid chromatography (HPLC), and B. aegyptiaca/chitosan nanoparticles were prepared. In vivo, evaluation tests were performed to assess the curative effect of the successfully prepared B. aegyptiaca/chitosan nanoparticles. For 30 days, the rats were divided into six groups, typical and fibrosis groups, where the liver fibrosis groups received B. aegyptiaca extract, silymarin, chitosan nanoparticles, and B. aegyptiaca/chitosan nanoparticles daily. In the current investigation, phenolic molecules are the major compounds detected in B. aegyptiaca extract. UV showed that the prepared B. aegyptiaca /chitosan nanoparticles had a single peak at 280 nm, a particle size of 35.0 ± 6.0 nm, and a negative charge at − 8.3 mV. The animal studies showed that the synthetic B. aegyptiaca/chitosan nanoparticles showed substantial anti-fibrotic protective effects against CCl4-induced hepatic fibrosis in rats when compared with other groups through optimization of biochemical and oxidative markers, improved histological changes, and modulated the expression of Col1a1, Acta2 and Cxcl9 genes, which manage liver fibrosis. In conclusion, the current research indicated that the prepared B. aegyptiaca/chitosan nanoparticles improved histological structure and significantly enhanced the biochemical and genetic markers of liver fibrosis in an animal model.