Physical activity in children and adolescents is on a decline trend. To this end, we conducted a matched-pair randomized controlled trial to examine the effects of a 4-week STAR (School-based; Train-the-trainer; Accessibility of resources; Recreational) skipping programme. 1,386 schoolchildren from 20 primary and secondary schools were recruited. Schools were randomized into the experimental or wait-list control group. Participants self-reported their health-related quality of life using the KIDSCREEN-27. Accelerometers were used to measure the time a subgroup of participants (n = 480) spent in moderate-to-vigorous physical activity during school hours on five consecutive days. Measures were taken at pre- and post-test. At post-test, students in the experimental group, compared to those in the control group, engaged in less moderate-to-vigorous physical activity during school hours. Health-related quality of life from two groups of students was similar, but the experimental group reported higher levels of autonomy and parent relationships. Results suggested that although the intervention did not increase students’ physical activity levels, it slightly improved their health-related quality of life. Future studies should explore personal factors that might mediate the effect of the intervention.