The study aimed to perform a systematic review with meta-analysis of randomized controlled trials (RCTs) to access the effects of red clover isoflavones on the blood lipid profile of both perimenopausal and postmenopausal women. PubMed, Web of Science, Scopus, SciELO, and Cochrane Library were searched for the terms ‘red clover’, ‘Trifolium pratense’, and ‘randomized controlled trial’ during November 2017. Summary measures were reported as weighted mean differences (WMD) with 95% confidence interval (CI). Fixed or random effects models were used for meta-analyses, according to heterogeneity. Risk of bias was measured with the Cochrane tool. Twelve RCTs (totalizing 1284 perimenopausal and postmenopausal women receiving red clover isoflavones for 4 weeks–18 months) resulted in a significant decrease in total cholesterol (WMD = −12.34 mg/dl; 95% CI: −18.21, −6.48), low-density lipoprotein cholesterol (WMD = −10.61 mg/dl; 95% CI: −15.51, −5.72), and triglycerides (WMD = −10.18 mg/dl; 95% CI: −16.23, −4.13) together with a significant increase in high-density lipoprotein cholesterol (WMD = 1.60 mg/dl; 95% CI: 0.17, 3.03). In conclusion, the results demonstrate that the ingestion of red clover may have a beneficial effect on the lipid profile of perimenopausal and postmenopausal women.