Substantial studies have shown that ω-3 polyunsaturated fatty acids (PUFAs) have various health-promoting effects, however, there are inconsistent results from animal studies which showed that ω-3 PUFAs have no effects or even detrimental effects. Emerging research suggests that oxidized ω-3 PUFAs have different effects compared with un-oxidized ω-3 PUFA, therefore, lipid oxidation of dietary ω-3 PUFAs could contribute to the mixed results of ω-3 PUFAs in animal studies. Here we prepared an AIN-93G-based, semi-purified, powder diet, which is one of the most commonly used rodent diets in animal studies, to study the oxidative stability of fortified ω-3 PUFAs in animal feed. We found that lowering the storage temperature or addition of a certain antioxidant, notably tert-butylhydroquinone (TBHQ), helps to stabilize ω-3 PUFAs and suppress ω-3 oxidation in the animal diet while reducing the level of oxygen in storage atmosphere is not very effective. Addition of 50 ppm TBHQ in the diet inhibited 99.5 ± 0.1 % formation of primary oxidation products and inhibited 96.1 ± 0.7 % formation of secondary oxidation products, after 10-day storage of the prepared diet at a typical animal-feeding-experiment condition. Overall, our results highlight that ω-3 PUFAs are highly prone to lipid oxidation in a typical animal feeding experiment, emphasizing the critical importance to stabilize ω-3 PUFAs in animal studies.