In this work, thymol was encapsulated in sodium caseinate using high shear homogenization. The transparent dispersion at neutral pH was stable for 30 days at room temperature as determined by dynamic light scattering and atomic force microscopy, which agreed with high ζ potential of nanoparticles. The slightly decreased particle dimension during storage indicates the absence of Ostwald ripening. When molecular binding was studied by fluorescence spectroscopy, thymol was observed to bind with tyrosine and possibly other amino acid residues away from tryptophan of caseins. At pH 4.6 (isoelectric point of caseins), the stabilization of thymol nanoparticles against aggregation was enabled by soluble soybean polysaccharide, resulting from the combined electrostatic and steric repulsions. The encapsulated thymol showed the significantly improved antilisterial activity in milk with different fat levels when compared to thymol crystals, resulting from the quicker mixing and increased solubility in the milk serum. The transparent thymol nanodispersions have promising applications to improve microbiological safety and quality of foods.