Aim This study objectively investigated the amount and intensity of German primary school children’s physical activity (PA) during different segments of the school day and explored the contribution of physical education (PE) and break times to daily moderate to vigorous PA (MVPA). Subject and methods PA of 294 children (7.1 ± 0.7 years, 48 % male) was objectively measured for 6 days using Actiheart®. Based on children’s timetables, break times and PE periods were determined and PA was calculated individually and subsequently classified in light (1.5–3 MET), moderate (3–6 MET) and vigorous (>6 MET) intensities. Weight status was determined during a school visit. Results Children spent 133 ± 61 min in MVPA; on weekdays, this amount increased significantly (141 ± 66 min, p ≤ 0.01). 45.9 % of children reached physical activity guidelines of 60 min of MVPA daily, with boys achieving this goal significantly more often than girls (65.6 vs. 28.7 %, respectively; p ≤ 0.01). PE lessons and break times accounted for 15 ± 13 min (12.7 %) and 7 ± 6 min (5.8 %) of daily MVPA, respectively. On days with PE, children spent 144 ± 68 min in MVPA, whereas on days without PE, this time decreased significantly to 122 ± 63 min (p ≤ 0.01). Conclusion The findings suggest that segments such as PE lessons and morning breaks are important sources for MVPA for boys and girls. This should therefore be considered for policies, timetables and curriculums in order to offer sufficient opportunities for children to be physically active during the school day.