Background: In our society, children are particularly vulnerable to physical inactivity and excessive sedentary time (ST). The aim of this study was to evaluate the effectiveness of a school-based intervention designed to promote physical activity (PA) and reduce ST in 6- to 10-years-old children from a disadvantaged neighborhood. Methods: The first intervention of this randomized trial was carried out in School 1 in 2017/2018 and 2018/2019, School 2 benefited from the same intervention in 2018/2019. Baseline assessments were realized using accelerometers prior to the intervention (T1-T2), after the first intervention (T3) and after the second intervention (T4). School-based actions targeted children, parents, teachers, physical, and organizational environment of school and politics. The chi-square test of independence was used to analyze the evolution of the moderate and vigorous physical activity (MVPA) and ST. Results: For School 1, an increase in the percentage of very active children (over 40 minutes MVPA/day) and of having a very low ST (less 240 minutes/day) (p = 0.00) was found. No further evolution was revealed during the intervention (T2-T3) and 1 year after (T3-T4). For School 2, similar effects on PA and ST were found at T3 (p < 0.05). Conclusions: Positive effects occurred before the intervention in each school and then remained stable.