Purpose: Schools provide opportunities for children to accumulate recommended daily moderate to vigorous physical activity (MVPA). This study aimed to determine physical activity (PA) across the school day among elementary school children in Qatar. Methods: This cross-sectional study recruited 181 Grade 1 (5.8 ± 0.4 years) and Grade 4 (9.0 ± 0.5 years) children. Participants wore wrist-based accelerometers for 5 days to assess school-based PA. MVPA during physical education, recess, and class time were compared across sex, grade, and body mass index using general linear models. Results: Only 39.0% of this cohort met the recommended 30 min of MVPA during school hours. Fewer girls (23.2%) than boys (58.1%) achieved the school-based PA guidelines (p < 0.001). The children engaged in 19.0 ± 12.3%, 19.3 ± 8.6%, and 6.2 ± 3.4% of the designated physical education, recess, and class time in MVPA, respectively. Conclusion: Elementary school children in Qatar engage in inadequate MVPA during the school day, especially girls. Enhancing PA opportunities during physical education and recess is crucial.