Introduction Physical activity (PA) plays an important role in the prevention of cardiovascular diseases, especially in children. Previous studies which investigated the role of PA and sedentary time (ST) in cardiovascular disease used different measurements and found inconsistent results. The current study used recommended standardized measures and provides an overview of PA and ST among Dutch primary school children and their associations with cardiovascular risk factors. Methods 503 children (55% girls, mean age (± SD) 10 ± 1y) were included. PA (total PA, lightPA and moderate to vigorous PA (MVPA)) and ST were measured with the Actigraph GT3X accelerometer. PA in different domains was measured with the BAECKE questionnaire. Cardiovascular risk factors included BMI z-score, waist circumference, blood pressure (z-score) and estimated cardiorespiratory fitness (CRF) as measured with the 20 meter shuttle run test. Results Children spent 57 ± 20 min/day (8%) on MVPA and 42% of the children reached the MVPA guideline of 60 min/day. Total PA and MVPA (h/day) were negatively associated with BMI z-score (B = -0.452, p = 0.011) and waist circumference (B = -3.553, p = 0.011) and positively associated with CRF (B = 2.527, p = <0.001). ST was positively associated with BMI z-score (B = 0.108, p = 0.048) and waist circumference (B = 0.920, p = 0.033). No significant associations were found between total PA or PA intensities and blood pressure. Conclusion This study used standardized measures of PA and therefore created an accurate overview of PA, ST and their associations with cardiovascular risk factors. PA and ST were associated with BMI z-score, waist circumference and CRF. The findings emphasize the importance of promoting MVPA in children, but also highlight the potential benefits of reducing ST to improve cardiovascular risk factors. Trial registration ClinicalTrials.gov NCT03440580.