The purpose of this study was to determine favorable physical activities, by intensity, type, and frequency that would serve to minimize the prevalence of metabolic syndrome. A total of 24,178 individuals participated in the Korean National Health and Nutrition Examination Survey that investigated the risk factors for metabolic syndrome and physical activity including the physical activity type (vigorous and moderate activity, walking, strength, and flexibility) and the frequency (numbers of days per weeks where physical activity lasted at least 10 min per session). Complex-samples analysis, descriptive statistics, Pearson’s Chi-square test, and multivariate logistic regression analyses were conducted to analyze the data. The results confirmed that physical activity had a favorable effect on reducing the occurrence of metabolic syndrome. The lowest prevalence of metabolic syndrome was observed when vigorous physical activity was conducted six times per week (OR 0.65, 95% CI 0.45–0.94). The associated beneficial effects included improvements in the risk factors of metabolic syndrome, depending on the specific physical activity type and frequency. Patients diagnosed, as having metabolic syndrome should be aware of the associated underling risk factors in order to determine a targeted physical activity intervention.Electronic supplementary materialThe online version of this article (doi:10.1186/s40064-016-3514-5) contains supplementary material, which is available to authorized users.