The pathogenesis and progression of Hypoxic-Ischemic Encephalopathy (HIE), a major cause of severe neurological disability and mortality in the perinatal period, is shaped by the interplay of multiple processes including inflammation, oxidative stress, and excitotoxicity. We conducted a longitudinal study determining biomarkers of oxidative stress and inflammation in non-invasive urine samples of newborns with moderate/severe HIE (N=51) employing Liquid Chromatography - Mass Spectrometry. We noted that levels of several biomarkers of oxidative stress increased over time demonstrating the ongoing propagation of oxidative injury. Prostaglandins, in contrast, showed a decreasing trend in their concentration profiles over time, which probably reflects their mediation on pathogenic mechanisms, including the inflammatory response. Statistically significant differences in the levels oxidative stress of neonates with distinct brain lesion patterns, as detected with Magnetic Resonance Imaging (MRI), were observed, revealing an increase of lipid peroxidation biomarkers in newborns with cerebral lesions (MRI score 1) as compared to scores 0 and 2. Moreover, a gender-dependent study showed no statistically significant differences in biomarker concentrations between male and female infants. Our observation leads to the hypothesis that the monitoring of non-invasive lipid peroxidation biomarkers could aid diagnosis and predicting of long-term outcomes as complementary tool to standard explorations.