Background Daily physical activity is vital for the health and development of children. However, many children are inactive. Previous attempts to achieve sustained increases in daily physical activity in children have been ineffective. Join Us: Move Play (JU:MP) is a whole-system, complex, community-based intervention aiming to increase the physical activity levels of children aged 7 to 11 years who live in areas of Bradford, England, which are multicultural and have high levels of deprivation. Objective The purpose of this quasiexperimental controlled trial is to assess whether the JU:MP program increases primary school children’s physical activity. Methods The study has a 2-arm, quasiexperimental, nonblinded, nonequivalent group design and will be conducted with primary school children aged 5 to 11 years at 3 timepoints, including baseline (before intervention), 24 months (during intervention), and 36 months (after intervention). Children attending primary schools within the intervention area will be invited to participate. Children attending similar schools within similar neighborhoods based on school and community census demographics (deprivation, free school meals, and ethnicity) outside of the JU:MP geographical area will be invited to participate in the control condition. At each timepoint, consenting participants will wear an accelerometer for 7 consecutive days (24 hours a day) to measure the primary outcome (average daily moderate-to-vigorous physical activity). Multivariable mixed effects linear regression will be applied to estimate differences in the primary outcome between the 2 arms at 24 months and 36 months on an intention-to-treat basis. The secondary outcome analysis will explore changes in socioemotional well-being (teacher reported), quality of life (parental/carer reported), and other contextual factors (parents/carer reported), as well as segments of the day activity, sleep, sedentary screen time, frequency of places to be active, parent practices (nondirective support and autonomy support), social cohesion, and neighborhood walking/exercise environment. Results Recruitment occurred from July 2021 to March 2022, and baseline data were collected from September 2021 to March 2022. As of March 2022 (end of baseline data collection), a total of 1454 children from 37 schools (17 intervention schools and 20 control schools) have been recruited. The first follow-up data collection will occur from September 2023 to March 2024, and the second and final follow-up data collection will occur from September 2024 to March 2025. Data analysis has not begun, and the final results will be published in December 2025. Conclusions This article describes the protocol for a quasiexperimental controlled trial examining a novel whole-system intervention. Trial Registration ISRCTN ISRCTN14332797; https://www.isrctn.com/ISRCTN14332797 International Registered Report Identifier (IRRID) DERR1-10.2196/43619