Age at natural menopause (ANM) has become an important health issue in older women. We explored secular trends in ANM in Korea during the past decade, and defined factors predicting ANM. A total of 12,761 naturally menopausal women were selected from the 2001 to 2014 data of the Korea National Health and Nutrition Examination Survey, stages II to VI. The participants were divided into four groups based on 5-year ANM categories: <45, 45 to 49, 50 to 54, and ≥55 years. To identify factors associated with ANM, the regression analysis was used. Both the mean (SE) and median (SE) ANM were 49.30 (0.07) years. The cumulative proportion of women experiencing menopause before the age of 40, 45, 50, and 55 years was 3.6%, 11.8%, 46.0%, and 90.3%, respectively. The mean (SE) ANM in women born in 1929 or earlier, and between 1930 to 1934, 1935 to 1939, 1940 to 1944, and 1945 to 1949, was 47.9 (0.3), 48.1 (0.2), 48.8 (0.2), 50.1 (0.2), and 50.5 (0.1) years, respectively (P < 0.001). Residence in a rural area (odds ratio [OR] 1.82), low weight status (OR 1.61), a history of or current smoking, a low educational level, being without a partner, and participating in at least moderate physical activity (OR 1.47, 1.33, 1.32, and 1.26, respectively) were more likely to result in an early ANM. Women with prior childbirth were less likely to experience early menopause (OR 0.34). In contrast, late menopause was associated with obesity and being overweight (OR 1.63 and 1.27). We found that the mean ANM exhibited upward secular trends. Socioeconomic status and lifestyle factors were the principal independent factors affecting ANM.