Background: Alhagi maurorum, commonly used in folk medicine, has been reported to have several biological activities. Objective: We have studied the antioxidant chemical components from A. maurorum to determine their in vitro antiproliferative and hepatoprotective activities. Materials and Methods: The alcoholic extract of A. maurorum root was subjected to a successive solvent fractionation and various chromatographic techniques guided by the 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging assay to isolate their antioxidant active compounds. The structures of the isolated compounds were identified through the extensive use of nuclear magnetic resonance and mass spectroscopy coupled with correlation to known compounds. The antioxidant and cytotoxic activities of the isolated compounds were quantified using DPPH and 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide assays, respectively. The hepatoprotective activity of each extract and the total flavonoid fraction were assessed quantitatively on carbon tetrachloride (CCl4)-induced hepatotoxicity in rats. Results: Fourteen flavonoids, including four aglycones (1–4) and ten glycosides (5–14), were isolated. The flavonoid glycosides (6–14) are being reported for the first time to our knowledge. The free aglycones, those of the flavonol type, exhibited strong antioxidant and antiproliferative activities. The flavonoid glycosides exhibited weak cytotoxic activity against the hepatocellular carcinoma cell line. The total flavonoid fraction showed the strongest hepatoprotective activity against CCl4-induced hepatotoxicity. Conclusion: A total of 14 flavonoids were identified from A. maurorum; nine of them were isolated for the first time. Flavonoids were the main chemical group identified from the A. maurorum root extracts, and they are responsible for the hepatoprotective activity. The findings set up a scientific explanation for the folkloric administration of A. maurorum in the treatment of hepatic disorders.