The hepatoprotective effect of β-Sitosterol (BSS), a natural phytosterol, after being formulated into a suitable pharmaceutical drug delivery system has not been widely explored. BSS was isolated from Centaurea pumilio L., identified and formulated as lipid-polymer hybrid nanoparticles (LPHNPs) using the poly(D,L-lactide-co-glycolide) polymer and DSPE-PEG-2000 lipid in different ratios. The selected formulation, prepared with a lipid: polymer: drug ratio of 2:2:2, had an entrapment efficiency (EE%) of 94.42 ± 3.8, particle size of 181.5 ± 11.3 nm, poly dispersity index (PDI) of 0.223 ± 0.06, zeta potential of −37.34 ± 3.21 and the highest drug release after 24 h. The hepatoprotective effect of the formulation at two different doses against CCl4 induced hepatotoxicity was evaluated in rats. The results showed that the BSS-LPHNPs (400 mg/kg) have the ability to restore the liver enzymes (alanine aminotransferase (ALT) and aspartate aminotransferase (AST)), liver lipid peroxidation markers (malondialdehyde (MDA) and catalase (CAT)), total bilirubin and albumin to their normal levels without inhibitory effect on the CYP2E1 activity. Also, the formulation could maintain the normal histological structure of liver tissue and decrease the cleaved caspase-3 expression. LPHNPs formulation encapsulating natural BSS is a promising hepatoprotective drug delivery system.