Introduction: Jaundice is the most common condition requiring medical attention in newborns. Phototherapy is the standard treatment for jaundice. However, in recent decades, phototherapy has been considered as an oxidative stress that can cause lipid peroxidation and damage to DNA. Accordingly, the present study was conducted to examine the possible effects of phototherapy on the Pro-oxidant/Antioxidant Balance (PAB) in jaundiced newborns. Methods: The present clinical trial was conducted on 70 icteric term neonates admitted to Ghaem Hospital of Mashhad, Iran between February 2013 and February 2015. The study population consisted of all term neonates who were admitted to the hospital within 2 to 14 days after birth for unconjugated hyperbilirubinemia (bilirubin levels > 15 mg/dl) and were treated with phototherapy. Neonates’ and mothers’ characteristics, along with the cause of jaundice, were collected through a researcher-made questionnaire, and neonates’ bilirubin levels and PAB values were simultaneously checked before, during and after the phototherapy. Finally, bilirubin levels and PAB values were compared using statistical methods. Results: According to the results, neonates’ underlying characteristics were not statistically different. The average and standard deviation of bilirubin levels and PAB values were, respectively, 18.90±2.97 and 16.29±9.83 (before phototherapy), 15.71±3.16 and 29.63±12.56 (during phototherapy), and 12.37 ±3.57 and 40.91 ±13.35 (after phototherapy). Conclusion: The results of this study demonstrate that decreased levels of bilirubin after phototherapy cause a shift in the PAB value in favor of oxidants.