Phytoestrogens are plant-derived substances similar to estrogens. Their chemical structure resembles endogenous estradiol, which is why they have similar mechanisms of action, but with a less potent effect. Relatively few studies explore their therapeutic application, although existing research suggests positive effects. Phytoestrogens can be used as supportive therapy for cycle control in temperamental sport mares, either as a replacement or supplement to gestagens. Due to the increasing use of phytoestrogens and so-called bioidentical hormones in human medicine as replacement therapy in postmenopausal women, whose effects are still under investigation, it is considered that results obtained in mares could serve as animal models for human reproduction. Besides positive effects on reproductive health, the therapeutic application of phytoestrogens brings numerous potential benefits to general health. Their pronounced anti-inflammatory, immunomodulatory, and osteoprotective effects are just some of the researched and confirmed impacts of these plant compounds. It is essential to conduct further research, especially on the long-term effects of phytoestrogens on the organism, as well as on the interactions between phytoestrogens and other drugs. Numerous positive effects, simplicity, and safety of phytoestrogen application, as well as their natural substitution for synthetic preparations, make phytoestrogens an attractive choice in therapeutic use. However, the use of phytoestrogens is recommended exclusively in consultation with a veterinarian.