BACKGROUND: High-sugar diets rich in fructose and other simple sugars are associated with increased lipogenesis and insulin resistance, potentially increasing the risk of metabolic syndrome, a condition closely linked with polycystic ovary syndrome (PCOS). This study aimed to evaluate the effects of a free sugar-restricted diet on anthropometric parameters, lipid profile, and glycemic control in women with PCOS. METHODS: In this randomized controlled clinical trial, 74 women aged 18-45 years with diagnosed PCOS were randomly assigned to either a free sugar-restricted diet group (n = 37) or a standard diet group (n = 37) for 12 weeks. Anthropometric indices, fasting blood glucose (FBG), serum insulin, insulin (HOMA-IR), insulin sensitivity (QUICKI), and lipid profile parameters including triglycerides (TG), total cholesterol (TC), low-density lipoprotein (LDL), and high-density lipoprotein (HDL) cholesterol were measured at baseline and at the end of the study. RESULTS: Compared to the control group, the intervention group showed significant reductions in body weight and body mass index (BMI) (P = 0.017 and P = 0.026, respectively). There was a significant reduction in FBG (P < 0.001) and an increase in QUICKI (P = 0.022) in the intervention group in comparison with control, though QUICKI lost significance after adjusting for confounders. Both groups experienced significant reductions in TC and LDL during 12 weeks, while TG levels decreased significantly only in the intervention group (P = 0.001). Between-group comparisons revealed a significant difference in TG (P = 0.037), and a near-significant difference in LDL (P = 0.054). After adjusting for confounders, lipid profile components, except for LDL, improved in the intervention group. CONCLUSIONS: This study showed that a 12-week free sugar-restricted diet can lead to weight reduction and improvements in blood glucose and lipid profile parameters in women with PCOS. TRIAL REGISTRATION: IRCT20230615058489N1; Iranian Registry of Clinical Trials ( https://www.irct.ir); Date of registration: June 25, 2023.