Introduction: School-based exercise interventions targeted at reducing obesity are often successful in the short term, but they are resource-heavy and do not always lead to long-lasting behaviour changes. This study investigated the effect of reducing sedentary time, rather than increasing exercise, on physical activity (PA) behaviours and obesity in primary school children. Methods: Thirty UK state primary schools participated in this cluster-controlled intervention study (IDACI score = 0.15 ± 0.07, free school meals = 26 ± 9%). Twenty-six intervention and 4 control schools (intervention = 3,529, control = 308 children) completed the Physical Activity Questionnaire for Children (PAQ-C) in terms 1 and 3. Three intervention and 3 control schools (intervention = 219, control = 152 children) also measured waist-to-height ratio (WTHR). The Active Movement Intervention is a school-based programme which integrates non-sedentary behaviours such as standing and walking in the classroom. Data were analysed via ANCOVAs and multiple linear regressions. Results: WTHR was reduced by 8% in the intervention group only (F(2, 285) = 11.387, p < 0.001), and sport participation increased by 10% in the intervention group only (F(1, 232) = 6.982, p = 0.008). Other PAQ-C measures increased significantly in the intervention group, but there was no group*time interaction. Changes in PAQ-C did not predict reductions in WTHR. Instead, the amount of change in WTHR was predicted by intervention group and by baseline WTHR of the pupil, where children with higher baseline WTHR showed greater reductions (F(2, 365) = 77.21, p < 0.001, R2 = 0.30). Socio-economic status (SES), age, or gender did not mediate any of the changes in the PAQ-C or WTHR. Conclusion: Reducing sedentary behaviours during school time can be an effective obesity reduction strategy for primary school children who are overweight. The lack of demographic effects suggests that this method can be effective regardless of the school’s SES, pupil age, or gender.