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Neonatal and juvenile foals are particularly susceptible to oxidative stress due to low circulating antioxidant levels at birth and a developing endogenous immune system. Vitamin E (α-tocopherol) and selenium provide complementary protection against membrane lipid peroxidation, acting directly as a radical scavenger and as an enzymatic catalytic cofactor of glutathione peroxidase (GPx), which neutralizes hydrogen peroxide and organic hydroperoxides using glutathione (GSH) as the electron donor. This study evaluated the effects of daily oral supplementation with natural RRR-α-tocopherol (Group 1, n = 10) versus synthetic all-rac-α-tocopherol (Group 2, n = 10) compared to an unsupplemented reference control group (Group 3, n = 10) on systemic antioxidant biomarker status in Arabian and Shagya Arabian foals undergoing primary West Nile Virus (WNV) vaccination at a Hungarian National Stud farm. Three biomarkers — plasma α-tocopherol, red blood cell α-tocopherol (vvtE), and whole blood glutathione (GSH) — were measured at three time points: baseline (T1), intermediate (T2), and post-vaccination (T3). Across all three groups, changes across time intervals (Δ = T3 − T1) were analyzed using linear mixed-effects models (lmer, R) with Tukey-adjusted pairwise comparisons, controlling for group, sex, and age. Natural α-tocopherol supplementation (Group 1) significantly preserved plasma α-tocopherol relative to unsupplemented controls (p = 0.0052), while synthetic α-tocopherol (Group 2) did not (p > 0.05). Both natural and synthetic α-tocopherol significantly increased erythrocyte membrane α-tocopherol (Group 1: p = 0.0026; Group 2: p = 0.0392). No significant treatment effect was observed for whole blood glutathione levels (p > 0.05 in all groups), consistent with physiological age-related maturation rather than supplement-driven change. A significant sex effect was detected for erythrocyte vitamin E only, with male foals demonstrating greater RBC α-tocopherol accumulation than fillies (p = 0.0455). These findings demonstrate the superior bioavailability of natural vitamin E for maintaining systemic circulating pools during immunization in foals and establish a baseline antioxidant reference point for physiological antioxidant fluctuations in foals.