Objectives: This study investigates whether Cloprostenol, a synthetic prostaglandin analog, could protect against ischemia/reperfusion (IR) injury in rat ovaries. Methods: Adult female rats were divided into four groups: Sham groups, ischemia (IS) groups, ischemia/reperfusion (IR) groups, and Cloprostenol-treated (CT) groups. The IR injury model was established by clamping the ovarian pedicle for a specified period, followed by reperfusion. The CT group received a pre-treatment of Cloprostenol before inducing ischemia. Ovarian tissues were collected for histological, and immunohistochemical examination. Results: The IS group exhibited severe morphological damage to ovarian tissues, including disrupted tissue architecture and increased apoptosis (p < 0.001). In contrast, the CT group displayed significantly improved ovarian histology, with notable preservation of ovarian tissue and reduced apoptotic activity (p < 0.01). Immunohistochemical analysis revealed that the levels of 8-Hydroxy-2-deoxyguanosine (8-OHdG), Caspase 3, Cyclooxygenase 2 (COX-2), and Interleukin 1 beta (IL-1 beta) staining, which were elevated in the IS and IR groups, were significantly diminished in the CT group (p < 0.05). Conclusion: Cloprostenol administration before IR injury in rat ovaries demonstrated a remarkable protective effect by improving histological damage and reducing DNA damage inflammation. These results highlight the therapeutic potential of Cloprostenol in safeguarding ovarian health against IR.