The effect of permitted antioxidants, including α-tocopherol, β-carotene, ascorbyl palmitate, ascorbic acid, citric acid, and their combinations, on the lipid oxidation of structured lipid (SL)-based infant formula (IF) was evaluated. The 3.5% oil-in-water IF emulsion was formulated with a human milk fat analogue enriched with docosahexaenoic acid and stearidonic acid, and the antioxidants were added at 0.005% and 0.02% of the oil. The peroxide value, anisidine value, and hexanal concentration of emulsion samples were measured over a 28-day period. The results showed that whether a compound exhibited antioxidant behavior depended on its mechanism of action, polarity, concentration, and environmental conditions. The most effective antioxidant was ascorbyl palmitate at 0.005%, and a synergistic antioxidant effect was found between α-tocopherol and β-carotene. A high correlation was observed between anisidine value and hexanal content. Our findings have important implications for the successful incorporation of SL into IF products for infant nutrition and health.