Lipid-soluble vitamin E (VE) and water-soluble vitamin B2 (VB2) can be encapsulated together in the same water–oil–water emulsion system. The ability of whey protein isolate (WPI)–polysaccharide complexes to synergistically control the release rates in such a system was investigated. The complexes studied were WPI–low methoxyl pectin (LMP) and WPI–κ-carrageenan (KCG). The encapsulation efficiency of VE and VB2 of the WPI system is 66% and 64% and increases by about 1.4- and 1.2-fold in the WPI–LMP and WPI–KCG complexes, respectively, which serve as selective non-pH-dependent barriers against enzyme attack. These complexes also greatly ameliorate the controlled release rates of both vitamins. The low-charge LMP, with its multiple protein- and oil-binding abilities, exhibits greater synergistic effects than the high-charge KCG.