Selenium (Se) is one of the essential elements for human health, where Se-containing compounds can prevent cancer and reduce mortality by regulating of the cell cycle and apoptosis. Exopolysaccharides from Fomes fomentarius have been used in traditional medicine to treat cancer. It appears that the combination of Se and fungal polysaccharides may be more effective. The effect of adding Na2SeO3 to the culture medium of the Iranian medicinal fungus F. fomentarius is investigated in this study. Adding 20 mg/L Na2SeO3 to the culture medium changed the F. fomentarius morphology and improved the structure of exopolysaccharides. Several methods, including FTIR, EDS, and ICP-OES, confirmed the presence of Se in the exopolysaccharides of F. fomentarius. The results demonstrated that the addition of Na2SeO3 increased the antibacterial activity against S.aureus (60%) and antioxidant activity (17.4%) significantly (p < 0.05). The cytotoxicity of these exopolysaccharides against 5637, A549, and KYSE30 cancer cells was also significantly increased (p < 0.05), and the viability of EPS-Se treated 5637 cells reached less than 10% after 72 h. Finally, F. fomentarius Se-polysaccharides can be used as a dietary supplement.