Objective Children's differences in moderate-to-vigorous physical activity levels are not at random. This study investigates the relevance of individual- and school-level characteristics in explaining these differences. Methods In total, 307 children (154 girls) aged 5–10 years, from 19 Portuguese schools, were sampled. Height and weight were measured, and body mass index was calculated. Time spent in moderate-to-vigorous physical activity was measured by accelerometry. Gross motor coordination was assessed with the KörperkoordinationsTest für Kinder battery and socio-economic status was obtained via the school social support system. School characteristics were obtained with an objective school audit. A multilevel analysis was used as implemented in Stata 15. Results Schools explained 18.2% of the total variance in moderate-to-vigorous physical activity, with the remainder being ascribed to children's distinct characteristics. Boys were more active (β =29.59±11.52, p <0.05), and having higher gross motor coordination levels (β =0.11±0.04, p <0.05) was positively associated with daily moderate-to-vigorous physical activity, whereas being older (β =−5.00±1.57, p <0.05) and having higher socio-economic status (β =−7.89±3.12, p <0.05) were negatively related with moderate-to-vigorous physical activity. From the school-level correlates, only playground dimension was significantly associated with moderate-to-vigorous physical activity levels. Children from schools with medium (40m2 to 69m2) and large playground dimensions (≥70m2) were less active than children with smaller playground dimensions (10m2 to 39m2). Conclusions Variation in school children's moderate-to-vigorous physical activity is mostly explained by their individual characteristics; school characteristics also play a role but to a smaller degree. Future intervention programs to change this behavior should be more personalized, emphasizing mostly individual-level characteristics.