This study is aimed at updating the relationships between physical activity (PA) and the metabolic syndrome (MetS) and/or insulin resistance (IR) in youth. Cross-sectional, prospective cohort and intervention studies, which examined the effect of PA on MetS, its components and IR in children and adolescents (<18 yrs), were searched by applying a combination of criteria in the PubMed database. The electronic search of studies published from 2000–2010 yielded >150 references. Of these, 37 studies were included. Twenty-six studies (70%) were cross-sectional observation studies, and two studies (8%) were prospective cohort studies. The remaining eight studies (22%) were interventions, of which three (<10% of all included studies) were randomized controlled trials. Commonly, higher PA levels were consistently associated with an improved metabolic profile and a reduced risk for MetS and/or IR in these populations. The impact of PA on MetS and/or IR appeared to be either independent of other factors, or alternatively or simultaneously mediated by the physical fitness and adiposity of youth. However, more-robustly designed interventions (i.e., some mega-randomized controlled trials based on lifestyle interventions) and additional cohort studies are required to make definitive inference about the magnitude and role of PA as a single genuine preventive and treatment strategy for the metabolic and cardiovascular risk of youth in the current obesogenic context.