Polycystic ovary syndrome (PCOS) is considered as one of the leading endocrine disorders during reproductive age in women. This study designed to determine the therapeutic effects of red clover (Trifolium pratense) on letrozole-induced PCOS in vivo. Forty female Sprague–Dawley rats were equally divided into five groups. Control group with a regular sexual cycle received normal saline (letrozole vehicle). Letrozole (1 mg/kg) was used to induce the PCOS to the rats in the treatment groups. After induction of PCOS, four treatment groups received the normal saline, or clomiphene citrate (1 mg/kg), or red clover extracts (500 or 750 mg/kg) for 30-days. After treatment, ovary and uterus were removed, weighed, and the ovaries were subjected to histopathological studies. Serum testosterone and estradiol levels, antioxidant activities, and lipid profiles were evaluated. Red clover extracts and clomiphene citrate decreased testosterone levels and showed a significant increase in estradiol levels in comparison to PCOS induced group (p<0.05). Red clover administration restored the GSH, SOD and CAT levels (p<0.05) and decreased the NO and MDA levels (p<0.05). Treatments caused no significant change in levels of TG, TC, and FBG factors when compared to PCOS induced group (P>0.05). However, red clover (750 mg/kg) significantly increased HDL and decreased LDL levels when compared to PCOS induced group (P<0.05). Treatment with red clover reduced ovarian weight, volumes of ovarian, medulla, cortex and number of cysts and increased number of oocytes compared to PCOS group. Both red clover and clomiphene citrate could treat the letrozole induced PCOS in rats; however, red clover indicated antioxidant activities more than clomiphene citrate. Red clover may be used for discovering anti-PCOS drugs with lower side effects.