Background Childhood obesity accompanied by lower levels of health-related physical fitness (HRPF) is a major threat to public health both internationally and locally. Children with intellectual disability, especially adolescents, have a higher risk of being overweight/obese and having poor HRPF levels. Therefore, more interventions are needed to help this population attain their optimal health levels. However, there has been relatively limited research on this population compared with on their typically developing peers. Objective The proposed study aims to fill this knowledge gap by developing and examining the success of a physical activity (PA) intervention for the target population. Methods The proposed study will be a 12-week, school-based randomized controlled trial. The participants (N=48) will be recruited from special schools for students with mild intellectual disability and then randomly allocated to either the intervention group (IG) or the wait-list control group (CG). During the intervention period, the participants in the IG will receive a fun game–based moderate-to-vigorous PA (MVPA) training program (2 sessions/week, 60 minutes/session, for a total of 24 sessions). The intensity of the activities will increase in a progressive manner. Participants in the CG will receive no program during the study period, but the same PA program will be provided to them after the completion of the study. To observe and evaluate the sustaining effects of the intervention, follow-up testing will be scheduled for the participants 12 weeks after the intervention concludes. The study outcomes will include primary outcomes (obesity- and fitness-related outcomes) and a secondary outcome (blood pressure). All of the measurements will be taken at 3 time points. After the follow-up tests, the same PA training program will be provided to the participants in the CG. Results This study is ongoing. The participants were recruited from October 2020 to November 2020. The total duration of the study is 13 months. Study results are expected at the end of 2021. Conclusions The proposed study is expected to reduce obesity and improve HRPF levels in children with intellectual disability. If proven effective, the intervention will be made accessible to more special schools and mainstream schools with students with intellectual disability. Furthermore, the study can serve as an example for international researchers, policy makers, and members of the public who are seeking to tackle the problem of obesity and poor HRPF among children with intellectual disability. Trial Registration ClinicalTrials.gov NCT04554355; https://www.clinicaltrials.gov/ct2/show/NCT04554355 International Registered Report Identifier (IRRID) PRR1-10.2196/25838