To examine the effects of the SELF-FIT intervention on students' moderate-to-vigorous physical activity (MVPA) and motivation in physical education (PE).In a clustered randomized controlled trial, 667 students (mean age = 14.4 years, SD = 0.78) from 26 schools (i.e., clusters) were randomized into either an experimental group or a wait-list control group. Students in the experimental group received the SELF-FIT intervention, a school-based intervention designed to infuse fitness and game-like elements into PE using self-determination theory principles, while those in the control continued their classes using usual practices. Intervention content was provided by teachers who received training from the research team. The primary outcome was percentage of time spent in MVPA during PE. Secondary outcomes included basic psychological need satisfaction, motivation towards PE, leisure-time MVPA, and mental well-being. Data were analyzed using multi-level regression analyses and pre-specified interactions were tested (i.e., group*time*sex).Positive intervention effects were found on MVPA during PE (B = 4.00, 95% CI [2.96, 5.04], d = 0.36). Regarding the participants' competence and autonomy need satisfaction, and autonomous motivation, the intervention effects were stronger in girls, compared to boys.Fitness infusion and game-like elements, employed according to self-determination theory principles, can enhance students' physical activity and motivation towards PE. This low-cost intervention has the potential to be scaled-up and disseminated in secondary schools.