The aim of this investigation is to examine the anticancer activities of Balanites aegyptiaca fruit extract with its biogenic silver nanoparticles (AgNPs) against colon and liver cancer cells. B. aegyptiaca aqueous extract was fractionated according to polarity and by biosynthesized AgNP. The cytotoxicity of the extract, semi-purified fractions, and the AgNPs was examined on noncancerous cell lines. The safer fraction was subjected to ultra-performance liquid chromatography-MS to identify the major active constituents. The anticancer activities of the nontoxic doses of all the used treatments were tested against HepG2 and CaCo2 cells. The nontoxic dose of the B. aegyptiaca (0.63 mg/ml) extract showed high anti-proliferative activities against HepG2 and CaCo2 with a percentage of 81 and 77%, respectively. The butanol fraction was safer than the other two fractions with 46.3 and 90.35% anti-proliferative activity against Caco2 and HepG2 cells, respectively. The nontoxic dose of AgNPs (0.63 mg/ml) inhibits both HepG2 and Caco2 cells with a percentage of 84.5 and 83.4%, respectively. In addition, AgNPs regulate the expression of certain genes with folding higher than that of crude extract. Saponin-coated AgNPs showed great abilities to select the most anticancer ingredient(s) from the B. aegyptiaca extract with a more safety pattern than the polarity gradient fractionation.