Sodium caseinate is a food-grade protein that has several functional properties, such as acting as an emulsifying and stabilizing agent in a colloidal delivery system. Nanostructured lipid carriers (NLCs) have been proven to be highly effective carriers for encapsulating bioactive compounds. In this research, several novel food-grade NLC systems based on sodium caseinate (as a protein surfactant), anhydrous milk fat (as a solid lipid), and vitamin E acetate (as a liquid oil) were developed as an encapsulant for vitamin D3. The D-optimal combined design was employed to optimize the effects of lipid phase ratios and protein concentrations on particle size and loading efficiency. The optimized formulation obtained from the predicted model was composed of 1% w/v caseinate protein and a 73.23/26.78 solid lipid/liquid oil ratio with a desirability function of 0.983. This optimum formulation showed the smallest particle size at 120.16 nm with a narrow size distribution of 0.208 and an encapsulation efficiency of 96.14%. The cytotoxicity study showed that the anticancer effect of the vitamin was improved after incorporation into the NLC structure. The current study suggests that this composition of biopolymeric surfactant and applied lipid matrix could be an effective, health-promoting, and promising carrier system for developing food-grade bioactive delivery systems.