Polycystic ovary syndrome (PCOS) is one of the most common gynecological endocrinopathies. Evidence suggest that flavonoids have beneficial effects on endocrine and metabolic diseases, including PCOS. However, high-quality clinical trials are lacking. We aimed to conduct a systematic review and meta-analysis of experimental studies to determine the flavonoids’ effects in animal models of PCOS. Three electronic databases including PubMed, Scopus, and Web of Science were systematically searched from their inception to March 2022. The Systematic Review Center for Laboratory Animal Experimentation’s risk of bias tool was used to assess methodological quality. The standardized mean difference was calculated with 95% confidence intervals as the overall effects. R was used for all statistical analyses. This study was registered in PROSPERO (registration number: CRD42022328355). A total of eighteen studies, including 300 animals, met the inclusion criteria. Our analyses demonstrated that, compared to control groups, flavonoid groups showed a significantly lower count of atretic follicles and cystic follicles and the count of corpus luteum was higher. A significant reduction in the luteinizing hormone (LH), LH/follicle-stimulating hormone (FSH), and free testosterone were observed in intervention groups. Nevertheless, there was no significant difference in the effects of flavonoids on the level of FSH, estradiol, and progesterone. Subgroup analyses indicated that the type of flavonoid, dose, duration of administration, and PCOS induction drug were relevant factors that influenced the effects of intervention. Current evidence supports the positive properties of flavonoids on ovarian histomorphology and hormonal status in animal models of PCOS. These data call for more randomized controlled trials and further experimental studies investigating the mechanism in more depth.