The aim of this study was to compare in-school and out-of-school physical activity within a representative sample. Socio-demographic, physical activity, and anthropometric data were collected from a random sample of children (250 boys, 253 girls) aged 3-16 years attending nine primary and two secondary schools. Actigraph GT1M accelerometers, worn for seven days, were used to estimate physical activity levels for in-school (typically 09.00-15.00 h), out-of-school (weekday), and weekend periods. Physical activity as accelerometer counts per minute were lower in school versus out of school overall (in school: 437.2 ± 172.9; out of school: 575.5 ± 202.8; P < 0.001), especially in secondary school pupils (secondary: 321.6 ± 127.5; primary: 579.2 ± 216.3; P < 0.001). Minutes of moderate-to-vigorous physical activity accumulated in school accounted for 29.4 ± 9.8% of total weekly moderate-to-vigorous physical activity overall but varied by sector (preschool: 37.4 ± 6.2%; primary: 33.6 ± 8.1%; secondary: 23.0 ± 9.3%; F = 114.3, P < 0.001). Approximately half of the children with the lowest in-school activity compensated out of school during the week (47.4%) and about one-third at the weekend (30.0%). Overall, physical activity during the school day appears to be lower than that out of school, especially in secondary school children, who accumulate a lower proportion of their total weekly moderate-to-vigorous physical activity at school than younger children. As low in-school activity was compensated for beyond the school setting by less than half of children, promoting physical activity within the school day is important, especially in secondary schools.