In this study, a typical tea polyphenol epicatechin (EC) was investigated for its impact on the oxidative stability of whey protein isolate (WPI) in a fish oil-fortified emulsion. The oil-in-water emulsion system consisted of fish oil (1%, w/w), WPI (6 mg/mL), and EC (0.1, 1, and 2 mM), and the oxidation reaction was catalyzed by Fenton’s reagent at 25 °C for 24 h. The results showed EC exhibited a dose-dependent activity in the reduction of lipid oxidation (TBARS) and protein carbonylation. A Western blot analysis demonstrated that protein lipoxidation was inhibited by EC via interrupting the covalent binding of lipid secondary oxidation products, MDA, onto proteins. In addition, protein lipoxidation induced a loss of tryptophan fluorescence, and protein hydrolysis was partially recovered by EC. The findings of this study provide an in-depth understanding of the performance of phenolic antioxidants in relieving lipid oxidation and subsequent protein lipoxidation in oil-containing dairy products.