Background: Stress in infancy has dramatic effects on different systems, including the nervous system, endocrine, immune, reproductive and etc. Objective: The purpose of this study was to investigate the effects of extract of Iranian propolis (EIP) on ovarian tissue and oxidative stress in rats with maternal separation stress. Materials and Methods: 48 immature female rats were divided randomly into six groups. 1) Control group, 2) Control group+saline, 3) Stress group, includes infants that were separated from their mothers 6 hr/day, the 4th, 5th and 6th groups consisted of infants who in addition to daily stress received 50, 100 and 200 mg/kg of EIP, respectively. Then serum corticosterone, 17-beta-estradiol, malondialdehyde, total superoxide dismutase, glutathione peroxidase and ferric reducing antioxidant power levels were measured. The ovarian sections were stained by H&E, PAS, and TUNEL methods and were studied with optical microscopy. Results: Stress increased the blood serum corticosterone levels and 17-beta-estradiol reduced significantly (p<0. 001) and EIP prevented from this changes (p<0. 01). EIP significantly increased the number of ovarian follicles, oocytes and oocytes diameter in neonatal rat following stress (p<0. 01). EIP also significantly decreased the number of atretic follicles, TUNEL+granulosa cells, malondialdehyde levels and increased ferric reducing antioxidant power, total superoxide dismutase and glutathione peroxidase serum levels in neonatal rats following stress. The dose of 200 mg/kg EIP was more effective. Conclusion: This Study showed that the Iranian Propolis significantly could prevent oxidative stress and histopathological changes in the ovary of the neonatal rat the following stress.