This study aimed to evaluate the association between menopause and blood mercury concentrations in South Korean women. Women aged ≥20 years who participated in the Korean National Health and Nutrition Examination Survey 2008-2011 were included in this study. Primary and secondary analyses included women aged ≥20 years (n = 1,642) and 45-55 years (i.e., perimenopausal; n = 325), respectively. For all analyses, the mercury levels were log-transformed. The linear regression model for mercury levels was adjusted for age, body mass index, household income, menopausal status, hormone replacement therapy, use of oral contraceptives, smoking history, alcohol intake, physical activity, number of pregnancies, serum ferritin levels, and fish consumption. After adjusting for covariates, log-transformed blood mercury levels were significantly lower in women who were menopausal [β-coefficient -0.1488; 95 % confidence interval -0.2586, -0.0389; P = 0.01) than in those who were premenopausal. A similar relationship was identified in perimenopausal women (β-coefficient -0.1753; 95 % confidence interval -0.3357, -0.015; P = 0.03). The blood mercury concentration was lower in postmenopausal women than in premenopausal women. There was a significant positive correlation between blood mercury concentrations and both the frequency of alcohol intake and serum ferritin levels.