For the last decades, endometriosis has been a major gynecological problem and a significant cause of infertility for women worldwide. It is estimated that the disease affects about 10–15% of all women of reproductive age and 70% of women suffering from chronic pelvic pain. At the same time, the incidence is about 40–60% in women with dysmenorrhea and 20–30% in women with subfertility. Despite the high percentage of affected women, endometriosis is still characterized by insufficient knowledge of the pathogenic processes, leading to the development and continuity of the disease. For this reason, there is a significant need for insight and understanding of the pathogenesis of endometriosis. This systematic review aims to present the latest data on the use of rats in endometriosis research and to explore how fertility is affected in rats with endometriosis. The methodology included a review of the available publications retrieved by a search in various scientific databases, such as PubMed, Scopus, Medline, and Google Scholar. The initial search generated 30 titles, with 10 articles fulfilling the inclusion criteria. In conclusion, several surgical techniques have been proposed to induce endometriosis, mainly using rats as the appropriate animal model. Studies in rats showed that endometriosis causes infertility and that pregnancy rates are lower for rats with endometriosis than those without endometriosis. In addition, rats with endometriosis have significant abnormalities in the structure of their oocytes as well as in the development of their embryos (genetic abnormalities).