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Background: Neonatal open-heart surgery induces profound oxidative stress, yet its perioperative dynamics remain incompletely characterized. This study quantified urinary 8-hydroxy-2'-deoxyguanosine (8-OHdG) and 8-isoprostane as markers of oxidative damage, and plasma α₁-microglobulin (A1M) as an endogenous antioxidant, while exploring the influence of pre- and intraoperative factors. Methods: In a prospective cohort of 40 term neonates with critical congenital heart defects undergoing open-heart surgery, serial urinary and plasma samples were collected perioperatively. Biomarker concentrations were analyzed using mixed-effects regression models to assess associations with postnatal age, sex, preoperative oxygenation, oxygen surge at bypass initiation, and cell-free hemoglobin in the prime solution. Results: Urinary 8-OHdG and 8-isoprostane increased following bypass separation; 8-OHdG remained elevated through postoperative days 0-2, while 8-isoprostane returned toward baseline by day 1. Plasma A1M declined at bypass initiation, recovered to preoperative levels at separation, and rose thereafter. Females exhibited higher A1M concentrations throughout. Longer time to surgery was associated with greater preoperative oxidative stress, and lower preoperative arterial pO₂ correlated with increased 8-isoprostane at bypass separation. No statistically significant associations were identified between intraoperative variables and biomarker levels, although the study was designed to be a hypothesis generating study and not powered to detect modest intraoperative effects. Conclusions: This exploratory study delineates distinct perioperative trajectories of oxidative stress and antioxidant response in neonates undergoing open-heart surgery, with surgical timing, preoperative hypoxemia, and sex emerging as relevant associations. No statistically significant associations were identified between intraoperative variables and biomarker levels; however, the study was hypothesis-generating in design and not powered to detect modest intraoperative effects.