Background: As there are different views on the effects of aminophylline on neonatal renal function, we intended to observe the effects of aminophylline on renal dysfunction in neonates with prenatal asphyxia. Methods: This randomized trial was conducted in the Obstetrics and Gynecology Hospital, Tehran, Iran, from June 2016 to May 2017, in neonates with moderate to severe asphyxia during birth. Fifty-six neonates were divided randomly into two groups. The intervention group received one dose of 5mg/kg slow intravenous aminophylline injection and the placebo group received 2 mL/kg of intravenous 10% solution of dextrose saline during the first hour of life. They were monitored and compared for renal functional indices, electrolytes, and complications of asphyxia during the three days of life. Results: The mean of Cr (37.9 ± 8.8 vs 38.5 ± 9.4 and 20.8 ± 4.8 vs 30.1 ± 5.2 μmol/L), GFR (21.55 ± 4.7 vs 20.25 ± 4.4 and 30.8 ± 7.1 vs 20.1 ± 6.5 mL/minute/1.73 m2 ), Na (135.1 ± 12.4 vs134.5 ± 11.2 and 128.9 ± 11.5 vs 134.2 ± 10.9 mEq/L), and urine output (98.2 ± 25 vs 96.8 ± 23 and 148.7 ± 35 vs 108.8 ± 20 cc) were in the aminophylline treated and placebo group on the 1st and 3rd days, respectively. The mean difference of Cr (-9.3 (-8.9; -9.7) μmol/L); (P = 0.02), GFR (10.7 (10.1; 11.3) mL/minute/1.73 m2 ) (P = 0.009), Na (-5.3 (-5.9; -4.7) mEq/L) (P = 0.002), and urine volume (39.9 (24.9; 54.9) cc) (P = 0.001) presented statistically significant differences on the third day between the intervention and placebo group. Conclusion: Aminophylline was effective in preventing renal dysfunction in neonates with asphyxia. Neonates who received aminophylline indicated a significant improvement in GFR and urine output on the first day of life.