Polycystic ovary syndrome (PCOS) is a multifactorial hormonal disorder accompanied by impairment of endometrial function and structure. Pomegranate is recognized for its role in normalizing the female sex hormones in PCOS with little known about its effect on the accompanying endometrial histological alterations. To assess the possible ameliorative role of pomegranate juice extract (PJE) on endometrial injury in a rat model of PCOS. Forty adult albino rats were equally divided into 4 groups; control, PJE-treated (400mg/kg/day for 3 weeks), letrozole-treated (PCOS) (1mg/kg/day for 3 weeks), and PJE & PCOS groups. Serum Follicle-stimulating hormone (FSH), Luteinizing hormone (LH), testosterone, estradiol, and tissue malondialdehyde (MDA) were assayed. Uterine samples were processed for histological staining with hematoxylin & eosin and Masson's trichrome stains, Ki67 and androgen receptor immunohistochemical staining, and scanning electron microscopy. PCOS group revealed a significant increase in serum FSH, LH, testosterone, estradiol, and tissue MDA. Uterine sections depicted various histological alterations in the endometrium with signs of inflammation. A significant increase in the endometrial collagen fiber content, as well as a significant upregulation in Ki67 and androgen receptor immunohistochemical expression were detected. Scanning electron microscopy showed a significant decrease in the mean number of pinopodes. Concomitant administration of PJE efficiently restored the studied biochemical, histological, and immunohistochemical parameters. PJE ameliorated PCOS accompanying endometrial histological alterations through its antioxidant, anti-inflammatory, anti-fibrotic, anti-proliferative, and anti-androgenic effects most probably due to its polyphenols content.