This study aimed to jointly analyse moderate-to-vigorous physical activity (MVPA) and sedentariness, and their correlates, in children within their school contexts, using a multivariate multilevel approach. The sample comprises 499 Portuguese children (284 girls) from 23 schools. MVPA and sedentary time were estimated by accelerometer. A set of predictor variables from both child and school levels was tested. Overall, schools explained a small amount of the total variance in both MVPA (5.6%) and sedentariness (3.2%), and a correlation coefficient of − 0.45 (p < 0.05) was found between MVPA and sedentariness at the child level. Number of siblings and socioeconomic status (SES) were significantly associated with both sedentariness (SES: β = 2.372 ± 1.183; siblings: β = − 8.127 ± 2.759) and MPVA (SES: β = − 1.535 ± 0.421; siblings: β = 2.822 ± 0.977), but with opposite signs. Body Mass Index (BMI) (β = − 4.804 ± 1.898) and sex (male) (β = 21.561 ± 3.496) were only associated with MVPA. None of the school correlates were statistically significant in their joint effects to simultaneously explain sedentariness and MVPA. These results suggest that although MVPA and sedentariness may be different constructs, they are correlated and this should be taken into account when designing strategies to reduce children’s sedentariness and increase their MVPA. In addition, the small effect of the school context on this relationship highlights the important roles of child and family characteristics.