The single nucleotide polymorphisms (SNPs) in the gene of breast cancer suppressor protein (BRCA1)-associated protein (BRAP) are significantly associated with coronary artery disease, but the molecular mechanisms are not understood. We examined the associations of the SNPs (rs11066001 and rs3782886) in BRAP with metabolic syndrome (MetS), which is a strong predictor of cardiovascular disease, and potential associations between these SNPs and factors related to inflammation. There were significant associations of both the SNPs with MetS [rs11066001, odds ratio (OR) 0.70, 95% confidence interval (CI) 0.51-0.96, p = 0.028; rs3782886, OR 0.69, 95% CI 0.50-0.94, p = 0.020] under a dominant model after age and gender adjustment. Both SNPs were significantly associated with waist circumference, plasma glucose, glycated haemoglobin, triglycerides and nonesterified fatty acid. Our data provide evidence that the SNPs (rs11066001 and rs3782886) in BRAP decrease the risk of MetS, and associations of the SNPs with various components of MetS are different. Moreover, there are significant associations of both the SNPs with nonesterified fatty acid that could be involved in the inflammatory activity of electronegative low-density lipoprotein.