Background: This study aimed to examine the association between physical activity (PA) and a total cardio metabolic risk (CMR) score in children aged 3–12 years. Secondary objectives were to examine the association between PA and individual CMR factors. Methods: A longitudinal study with repeated measures was conducted with participants from a large primary care practice-based research network in Toronto, Canada. Mixed effects models were used to examine the relationship between parent-reported physical activity and outcome variables (total CMR score, triglycerides, glucose, high-density lipoprotein cholesterol, systolic blood pressure, waist circumference, weight-to-height ratio, and non-high-density lipoprotein cholesterol). Results: Data from 1885 children (6.06 y, 54.4% male) with multiple visits (n = 2670) were included in the analyses. For every unit increase of 60 minutes of PA, there was no evidence of an association with total CMR score (adjusted: −0.02 [−0.014 to 0.004], P = .11]. For the individual CMR components, there was evidence of a weak association between PA and systolic blood pressure (−0.01 [−0.03 to −0.01], P < .001) and waist-to-height ratio (−0.81 [−1.62 to −0.003], P < .001). Conclusion: Parent-reported PA among children aged 3–12 years was not statistically associated with total CMR, but was weakly associated with systolic blood pressure and waist-to-height ratio.