To assist the development of new therapeutic strategies for several disorders, biologically active peptides/proteins obtained from plant sources can be considered. Current study expected to determine the biological activities of peptide fractions of Mucuna pruriens against hepatocellular carcinoma cell lines (HepG2/ADM, HepG2, SMMC‐7721, and QGY‐7703), as well as normal cell line to prove their selectivity. Moreover, anti‐genotoxicity and antiviral activity against the hepatitis C virus (HCV) were assessed. The methods of this study were to isolate the peptides of M. pruriens and hydrolysate fractionation via fractionated pepsin‐pancreatin hydrolysates by ultrafiltration/high‐performance ultrafiltration cell, identify anti‐hepatoma activity of peptide fractions human liver cancer and normal cells by (3‐(4,5‐dimethylthiazole‐2‐yl)‐2,5‐biphenyl tetrazolium bromide) (MTT) assay, determine anti‐HCV, and assess anti‐genotoxic effect of peptide fractions against damage that induced via alkylating agent methyl methanesulphonate in human mononuclear cells. The results showed that the fraction 5–10 kDa has been reported to exhibit significant cytotoxic activity against HepG2 and QGY‐7703. It was proven that both of 5–10 and >10 kDa fractions are active against HCV. The cytotoxic concentration (CC50) of 5–10 kDa against the cell line was 703.04 ± 5.21 µg/ml. Anti‐genotoxic activities of the peptide fractions were evaluated as mean values for the analyzed comet images. In this regard, the highest activity of protecting DNA damages was observed by the peptide fraction of 5–10 kDa. This study revealed the potential ability of peptide fractions of M. pruriens for the treatment of liver cancer, HCV, and high activities of protecting DNA damages.