Cystic ovarian disease (COD) with uterine abnormalities is a postpartum reproductive pathology in Egyptian buffaloes causing significant economic losses. In this study, we aimed to employ various diagnostic methods for detecting cystic ovarian disease (COD) in Egyptian buffaloes. tour study assessed the effectiveness of the GnRH/PGF2α protocol as a treatment strategy. Our goal was to determine if this protocol could effectively reduce economic losses associated with cystic ovarian disease and improve herd fertility in Egyptian buffaloes. Eighty Egyptian buffalo cows were included in this study. They were identified to have follicular cysts through rectal examination, which was confirmed by ultrasonography. These buffaloes were then divided into two main groups: the COD Control (untreated) (GA) (n = 40) and COD group (GB) (n = 40) treated with GnRH/PGF2α. According to our immunological studies, buffaloes in the COD-treated group (GB) exhibited significantly lower serum levels of pro-inflammatory cytokines (IL-6, IL-1β, and TNF-α) compared to the control group. This observation was consistent with the decline in E2 levels and the increase in P4 levels (p < 0.01–0.001) observed in the treated animals compared to the untreated group. Furthermore, serum cortisol and glucose concentrations decreased in COD-treated buffaloes. Histopathological examination of ovaries and uterine tissue from slaughtered COD buffaloes has revealed significant structural alterations. These include the presence of ovarian cysts of varying sizes with vacuolar degeneration. Additionally, lymphoplasmacytic endometritis was observed in the uterine tissue of affected animals, featuring degeneration and desquamation of the endometrial lining accompanied by infiltration of mononuclear inflammatory cells. Severe and prolonged cases of COD, which did not respond to treatment, exhibited marked adverse pathological changes upon histopathological assessment of the genital tract. In conclusion, hormonal treatment with GnRH/PGF2α appears to be effective in treating COD-affected animals. The study provides valuable insights into the immunological, biochemical, and histopathological aspects of cystic ovaries associated with uterine disorders in Egyptian buffaloes, while also evaluating hormonal treatment for cystic ovarian disease as a means to minimize economic losses and improve herd fertility in this species.