Background Variability exists in children’s activity patterns due to the association with environmental, social, demographic, and inter-individual factors. This study described accelerometer assessed physical activity patterns of high and low active children during segmented school week days whilst controlling for potential correlates. Methods Two hundred and twenty-three children (mean age: 10.7 ± 0.3 yrs, 55.6% girls, 18.9% overweight/obese) from 8 north-west England primary schools wore ActiGraph GT1M accelerometers for 7 consecutive days during autumn of 2009. ActiGraph counts were converted to minutes of moderate (MPA), vigorous (VPA) and moderate-to-vigorous (MVPA) physical activity. Children were classified as high active (HIGH) or low active (LOW) depending on the percentage of week days they accumulated at least 60 minutes of MVPA. Minutes spent in MPA and VPA were calculated for school time and non-school time and for five discrete school day segments (before-school, class time, recess, lunchtime, and after-school). Data were analysed using multi-level modelling. Results The HIGH group spent significantly longer in MPA and/or VPA before-school, during class time, lunchtime, and after-school (P < .05), independent of child and school level factors. The greatest differences occurred after-school (MPA = 5.5 minutes, VPA = 3.8 minutes, P < 0.001). MPA and VPA were also associated with gender, BMI z-score, number of enrolled children, playground area per student, and temperature, depending on the segment analysed. The additive effect of the segment differences was that the HIGH group accumulated 12.5 minutes per day more MVPA than the LOW group. Conclusions HIGH active children achieved significantly more MPA and VPA than LOW active during four of the five segments of the school day when analyses were adjusted for potential correlates. Physical activity promotion strategies targeting low active children during discretionary physical activity segments of the day, and particularly via structured afterschool physical activity programs may be beneficial.