Background: Perinatal asphyxia is a major cause of neonatal morbidity and mortality, often leading to multi-organ dysfunction. It can alter the hypothalamic-pituitary-thyroid axis, affecting thyroid hormones (T3, T4, TSH) crucial for neurodevelopment. This study aims to assess thyroid hormone levels in neonates with birth asphyxia at a tertiary care centre of southern Rajasthan. Methods: A hospital-based case-control study was conducted in the NICU of RNT Medical College, Udaipur, over one year. Seventy-five term neonates with perinatal asphyxia (cases) and seventy-five healthy term neonates (controls) were enrolled. Cases were diagnosed based on clinical criteria and Apgar score <7 at 10 minutes. Serum T3, T4, and TSH levels were measured within 24 hours and at 72 hours of life using chemiluminescent immunoassay. Data were analysed using appropriate statistical tests, with p <0.05 considered significant. Results: Within the first 24 hours of life, mean serum levels of T3, T4, and TSH were comparable between asphyxiated and control neonates, with no statistically significant differences observed (T3: 2.39 ± 0.54 vs 2.31 ± 0.71 nmol/L, ; T4: 116.67 ± 24.18 vs 114.10 ± 21.59 nmol/L, TSH: 6.91 ± 1.46 vs 6.92 ± 1.35 mIU/L). By 72 hours, a significant decline in thyroid hormone levels was noted in asphyxiated neonates compared to controls. Mean T3 and T4 concentrations were markedly lower in cases (T3: 1.51 ± 0.73 vs 2.19 ± 0.69 nmol/L; T4: 76.82 ± 25.50 vs 117.27 ± 22.70 nmol/L). TSH levels also decreased significantly in cases relative to controls (5.97 ± 2.81 vs 7.46 ± 2.15 mIU/L), suggesting a blunted hypothalamic-pituitary-thyroid response. Conclusion: Perinatal asphyxia significantly suppresses thyroid function by 72 hours of life, as evidenced by a marked reduction in T3, T4, and TSH levels in affected neonates compared to controls. These findings indicate a blunted hypothalamic-pituitary-thyroid response, highlighting the importance of monitoring thyroid status in asphyxiated term neonates for timely intervention.