This study investigated the effects of the GLAMA (Girls! Lead! Achieve! Mentor! Activate!) and BLAST (Boys! Lead! Activate! Succeed Together!) controlled 8-week peer-led stealth intervention on school connectedness and physical activity self-efficacy (PASE). The GLAMA and BLAST sessions were conducted during curriculum time in an Australian state secondary school by 49 Year 10 student leaders and 206 Year 7 students. Year 7 school connectedness decreased in both the control and intervention schools (p<0.001). Baseline social self-efficacy was the largest single predictor of change in Year 7 school connectedness (p<0.001). PASE increased in both schools over the 8-weeks (p=0.054), with the intervention school improving more. School connectedness may require greater time to elicit positive changes and integrated curriculum approaches that include ongoing peer mentoring are warranted. As school connectedness is a protective factor for many public health outcomes, a stealth approach requires further investigation particularly exploring the role of process motivators.