The experimental data on the oral toxicity of nanostructured amorphous silica (SiO2), widely used in food supplements, pharmaceuticals, and cosmetics, in terms of its in vivo effect on the immune system, are contradictory. Therefore, this study aimed to assess the rat’s immune function after SiO2 oral administration. In the first experiment, SiO2 was daily orally administered to Wistar rats for 92 days in doses of 0.1, 1.0, 10, and 100 mg/kg of body weight (bw). In the second 28-day experiment, SiO2 in a dose of 100 mg/kg bw was daily orally administered to rats parenterally immunized with the food allergen ovalbumin (OVA) for the reproduction of systemic anaphylaxis reaction. Together with integral indices, we assessed intestinal permeability to protein macromolecules; hematology; CD45RA+, CD3+, CD4+, CD8+, and CD161a+ cells; cytokines TNF-α, IL-6, and IL-10; and IgG to OVA. The results obtained showed that SiO2 has no effect on the severity of the anaphylactic reaction, but is capable inducing a toxic effect on the T-cell immune systems of rats. Estimated no observed adverse effect level NOAEL for SiO2 ranges up to 100 mg/kg bw in terms of its daily consumption for 1–3 months. Using SiO2 as a food additive should be the subject of regulation.