The current results show that epigallocatechin-3-gallate (EGCG), in the form of phenolic anions at pH 8.0, can effectively disperse selenium nanoparticles. However, at gastric juice pH (1.0), the EGCG-dispersed selenium nanoparticles (referred to as E-Se) extensively aggregated, so that nano features largely disappeared. This demonstrates that deprotonated phenolic anions of EGCG play an important role in maintaining E-Se stability and suggests that E-Se would suffer from reduced oral bioavailability. To validate this conjecture, size-equivalent E-Se and bovine serum albumin (BSA)-dispersed selenium nanoparticles (B-Se), whose physicochemical properties were not altered at pH 1.0, were orally administered to selenium-deficient mice. In comparison to B-Se, the bioavailabilities of E-Se as indicated with hepatic and renal glutathione peroxidase activity and hepatic selenium levels were significantly (p < 0.01) reduced by 39, 32, and 31%, respectively. Therefore, the present study reveals that size-equivalent selenium nanoparticles prepared by different dispersers do not necessarily guarantee equivalent oral bioavailability.