Polycystic ovary syndrome (PCOS) is associated with insulin resistance and dyslipidemia. Pomegranate juice is a rich source of polyphenols that may improve blood pressure, lipid profile, and other risk factors of cardiovascular diseases (CVDs). No study has examined the effects of pomegranate juice consumption on the clinical outcomes of PCOS. This study aimed to examine the effects of concentrated pomegranate juice (CPJ) consumption on risk factors of CVDs in women with PCOS. In this randomized clinical trial, 44 PCOS women with an age range of 18-40 years and body mass index (BMI) of ≥25 kg/m were recruited. They were randomly allocated to the CPJ (n = 22) and control (n = 22) groups, and followed for 8 weeks. Anthropometric measures, blood pressure, and biochemical parameters were measured at baseline and at the end of the trial. Compared with the control group, CPJ consumption significantly reduced systolic (-9.77 ± 1.46 vs. -1.18 ± 1.46 mmHg, p < .001) and diastolic (-3.87 ± 1.36 vs. 0.30 ± 1.36 mmHg, p = .05) blood pressure, serum triglyceride (TG) levels (-7.82 ± 6.32 vs. 16.63 ± 6.32 mg/dl, p = .01), TG/high-density lipoprotein-cholesterol (HDL-C) ratio (-0.39 ± 0.24 vs. 0.66 ± 0.24, p = .007), and increased serum concentrations of low-density lipoprotein-cholesterol (LDL-C) (6.03 ± 2.47 vs. -1.98 ± 2.47 mg/dl, p = .04) and HDL-C (1.93 ± 1.10 vs. -1.78 ± 1.10 mg/dl, p = .03). These findings were obtained after taking baseline measurements and potential confounders into account. No adverse event or complication was reported due to CPJ consumption throughout the study. We found that CPJ consumption has a beneficial effect on blood pressure, serum concentrations of TG and HDL-C, and TG/HDL-C ratio in women with PCOS. However, this juice could increase serum LDL-C levels in these patients. This trial was registered at www.irct.ir as IRCT20191109045383N1.© 2020 John Wiley & Sons, Ltd.