Children’s engagement in physical activity of a vigorous intensity or higher is more effective at promoting cardiorespiratory fitness than moderate physical activity. It remains unclear how higher intensity physical activity varies between days when schoolchildren participate in physical education (PE) and non-PE days. The purpose of this study was to assess how PE contributes to sedentary behaviour and the intensity profile of physical activity accumulated on PE days compared to non-PE days. Fifty-three schoolchildren (36 girls, 11.7 ± 0.3 years) completed five-day minute-by-minute habitual physical activity monitoring using triaxial accelerometers to determine time spent sedentary (<1.5 Metabolic Equivalent of Tasks (METs)) and in light (1.5–2.9 METs), moderate (3–5.9 METs), vigorous (6–8.9 METs), hard (9–11.9 METs) and very hard intensity (≥12 METs) physical activity on PE days and non-PE days. Sedentary time was higher on non-PE days than on PE days (mean difference: 62 minutes, p < 0.001). Hard and very hard intensity physical activity was significantly higher on PE days compared with non-PE days (mean total difference: 33 minutes, all significant at p < 0.001). During the PE lesson, boys spent more time in hard (p < 0.01) and very hard (p < 0.01) physical activity compared to girls. Schoolchildren spent significantly more time in higher intensity physical activity and significantly less time sedentary on PE days than on non-PE days. As well as reducing sedentary behaviour, the opportunity to promote such health-promoting higher intensity physical activity in the school setting warrants further investigation.