A great number of prospective studies have investigated the relationship between leisure time physical activity (LTPA) and metabolic syndrome (MetS) risk. However, the results have been inconsistent. The aim of this study was to clarify the relationship between LTPA and MetS risk. Literature databases were searched including PubMed and Embase up to June 2013. A total of 17 studies, including 64,353 participants and 11,271 incident cases, were included in the meta-analysis. A high level of LTPA was statistically associated with decreased risk of MetS [high vs. low: relative risk (RR) = 0.80, 95 % confidence interval (CI) 0.75-0.85], whereas a moderate level of LTPA was weakly associated with decreased risk of MetS (moderate vs. low: RR = 0.95, 95 % CI 0.91-1.00). Subgroup analyses indicated that the association between a moderate level of LTPA and decreased risk of MetS was only significant in men (moderate vs. low: RR = 0.88, 95 % CI 0.81-0.97) and in studies with more than a 10-year follow-up period (moderate vs. low: RR = 0.90, 95 % CI 0.84-0.97). A high level of LTPA was statistically associated with decreased risk of MetS in each subgroup. A higher level of LTPA is associated with a lower risk of MetS. These findings could have public health implications with regard to prevention of MetS through lifestyle interventions.