To date, little research has longitudinally examined young children's physical activity (PA) during school hours, nor questioned children's perceptions of their own PA behaviours. This study investigated 20 children's actual physical activity levels (APA) and their perceived physical activity levels (PPA) (10 infants, mean age 6.6 years; 10 juniors, mean age 9.5 years). APA was evaluated using accelerometers across 36 whole school days (371 min per day); 18 days included Physical Education (PE) lessons and 18 did not. A repeated-measures three-factor ANOVA analysed: type of day; age phase; parts of the day and sex. PPA was collected by an interactive handset and an adapted version of the PA Questionnaire for Children (PAQ-C). Participants undertook 10 more minutes of moderate to vigorous PA (MVPA) on PE days (53 ± 19 min) compared to non-PE days (43 ± 15 min) (F = 92.32, p < 0.05) and only junior boys reached daily MVPA recommendations (60 ± 13 min) on PE days. Juniors over-estimated, and infants under-estimated, their APA levels. Educators need more support to teach and embed different PA intensities into the school day to enable children to better understand the health benefits associated with varying the intensity of their PA during school hours.