Despite physical education's health enhancing potential, students' activity levels in lessons are low. We evaluated a school-based intervention that involved rope skipping on students' moderate-to-vigorous physical activity (MVPA) in physical education. The intervention was evaluated using a clustered randomized controlled trial in 24 classes (N = 731 students; M = 14.38 years; all from Secondary 2) from 12 Hong Kong schools during September to December 2013. The primary outcome was percentage of lesson time spent in MVPA. Secondary outcomes included students' vigorous activity, counts per minute, perceived autonomy support and motivation for physical education. Accelerometer-based activity measures were taken from a sub-sample of 168 students during lessons 1 to 3 (baseline) and lessons 5 to 7 (treatment phase). Participants self-reported motivation variables at lessons 4 and 8. Teachers allocated to the experimental group included an intervention during treatment phase; those in the control group continued usual practices. The intervention involved a 15-minute rope skipping activity where students completed intervals of skipping with rests in between. Using multilevel modeling, we examined the intervention effects on measured outcomes, and whether effects differed for boys and girls. Overall intervention effects were not found. However, girls in the intervention group spent more time in MVPA (β = 0.25) and had higher counts per minute (β = 0.32) than control group counterparts at treatment phase. Perceived autonomy support and motivation variables were similar across groups. The intervention increased activity levels of girls, but not boys. Implementation of the intervention may reduce differences between boys' and girls' physical education activity levels. Trial registration: ANZCTR: ACTRN12613000968774. Copyright © 2017 Elsevier Inc. All rights reserved.