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Background Neonatal bilirubin encephalopathy (kernicterus) results from toxic accumulation of unconjugated bilirubin in the brain, often leading to irreversible neurological damage. Docosahexaenoic acid (DHA), an omega-3 fatty acid with anti-inflammatory and antioxidant properties, may attenuate bilirubin-induced neuropathological alterations in neonates. Objectives This study evaluated whether DHA mitigates neuropathological and molecular changes in a rodent model of bilirubin-induced encephalopathy via the CTBP1/miR-155-5p/KDM5A pathway and oxidative stress regulation. Methods In a cross-sectional experimental study, 48 neonatal Sprague-Dawley rats (7 days old) were allocated to Control, bilirubin encephalopathy (BE) and BE + DHA groups ( n = 16 each). Bilirubin (120 mg/kg i.p.) was administered to induce encephalopathy. DHA (100 mg/kg by gavage) was given daily for 3 days. Physical status, neuro-behavior (righting reflex, negative geotaxis), biochemical markers (serum bilirubin, neuron-specific enolase [NSE], oxidative stress indices), and histopathology were assessed. Gene and protein expression of CTBP1, KDM5A and miR-155-5p were measured (RT-qPCR, Western blot). Results DHA improved neurobehavioral scores and was associated with a faster decline in serum bilirubin levels during the later observation period. Serum bilirubin peaked at ∼15 μmol/L at 24 h in BE and declined to 10 μmol/L by 72 h, whereas DHA accelerated clearance to ∼5 μmol/L at 72 h (control ∼5 μmol/L). Brain bilirubin and NSE were significantly elevated in BE and mitigated by DHA (each ∼60% reduction vs. BE, p < 0.01). DHA also reduced cortical apoptosis (TUNEL-positive cells ∼10% vs. 25% in BE, p < 0.01). Molecular analysis showed bilirubin-induced upregulation of miR-155-5p (∼3-fold) with downregulation of CTBP1 and KDM5A (∼50–60% of control); DHA partially restored CTBP1/KDM5A levels and lowered miR-155-5p (∼1.4-fold, p < 0.01 vs. BE). Markers of oxidative stress and ferroptosis were elevated in BE (e.g., malondialdehyde + 175%, p < 0.001) and blunted by DHA (+ 50% vs. control, p < 0.01). Conclusion DHA administration significantly attenuated bilirubin-induced neurotoxicity in neonatal rats. Neuroprotection by DHA was associated with changes in the CTBP1/miR-155-5p/KDM5A axis and reduced oxidative stress–related markers.