Background & Aims: Polycystic ovary syndrome (PCOS) is one of the most common endocrine disruptions. As a result, treatments with little or no side effects such as herbal medicines and exercise have received special attention. The purpose of this study was to investigate the effect of 12-week Pilates training and Ginger supplementation on polycystic ovary syndrome in women. Materials & Methods: In this quasi-experimental study with pre-test and post-test design, 40 women with polycystic ovary syndrome participated in the study voluntarily and they were randomly divided into 4 groups including control, Pilates exercise, combined (Exercise + Ginger supplement), and Ginger supplementation. The exercise intervention groups performed Pilates exercises for 12 weeks and the supplementation group consumed 1 g of ginger capsules three times per day. Plasma levels of LH, FSH, SHBG, testosterone, and insulin were measured before and 12 weeks after intervention. Data were analyzed by SPSS software using covariance analysis and Tukey post hoc test at 5% significance level. Results: The results showed that LH (p<0.05), testosterone (p<0.05), and insulin (p<0.05) levels decreased in the intervention groups compared to the control group. The FSH (p<0.05) and SHBG (p<0.05) indices in the intervention groups were significantly higher than the control group. Also, the findings indicated the effect of treatments on the indices studied (p<0.05). While the combined treatment had the greatest effect, there was no significant difference between the exercise group and ginger supplementation group (p>0.05), except in the weight index that the superiority was observed with the exercise group (p<0.05). Conclusion: The results of this study showed that Pilates training and ginger supplementation can have beneficial effects on ovarian function and it is suggested as a therapeutic method to improve the status of patients with polycystic ovary syndrome. Keywords: Pilates training, polycystic ovary