Background: Polycystic Ovary Syndrome (PCOS) increases the risk of cardiovascular diseases and diabetes, and obesity can accelerate this trend. Objectives: This study aimed at determining the effect of prebiotics on anthropometric indices in patients with this syndrome. Methods: This controlled clinical trial was conducted with 62 women from 18- to 45-year-old in the city of Tabriz, Iran, during years 2016 to 2017. Participants were assigned to prebiotic and control groups, using the random blocks method. The intervention group had a daily intake of 20 g of resistant Dextrin, dissolved in a glass of water for three months, and the placebo group had a daily intake of 20 g of Maltodextrin, dissolved in a glass of water for three months. Participants' Body Mass Index (BMI), weight, waist circumference, and hip circumference were measured before, and three and six months after the intervention. Results: There was no significant difference between the groups in terms of baseline values (P > 0.05). Three months after the intervention, mean (SD) waist circumference, hip circumference, weight, and BMI was 78.11 (9.7), 100.85 (7.7), 65.31 (10.9), and 24.41 (4.2) in the prebiotic group and 86.54 (12.3),108.72 (10.7), 73.25 (14.7), and 27.73 (5.7) in the control group, respectively. Six months after the intervention, mean (SD) anthropometric indices was 78.11(7.9),101.45 (7.2), 65.70 (10.3), and 2 4.5 4 (3.9) in the prebiotic group and 86.4 (12.6), 108.54 (10.8), 73.8 (14.7), and 27.65 (5.5) in the control group, respectively. According to the Analysis of Variance (ANOVA) test, and with controlled baseline values, all anthropometric indices were significantly lower in the prebiotic group compared to the control group at three (P < 0.001) and six months (P < 0.001). Conclusions: This study confirmed the positive and significant effects of prebiotics in reducing anthropometric indices, three and six months after the intervention in women with PCOS.