Educational initiatives and actions are needed to provide students with skills to create active habits and lifestyles in order to increase the physical activity and fitness levels of young people. The main objective of this study was to analyse the effects of a classroom-based physical activity and life skills programme on students’ physical activity and fitness levels. The sample consisted of 65 students in the 6th grade of Primary Education, aged between 11 and 13 years (11.86 ± 0.53), divided into a control group (CG) and an experimental group (EG) for convenience and accessibility. This was a quasi-experimental, repeated measures, longitudinal cut-off research design. For 16 weeks, an interdisciplinary educational programme based on a combination of classroom-based physical activity and life skills was implemented. The results showed that the educational programme had a positive effect on students’ physical activity levels during school hours, specifically on reducing sedentary time (p< 0.001) and increasing light (p< 0.001) and moderate-to-vigorous (p< 0.001) physical activity. Positive effects were also found on the variables of explosive strength (p< 0.05) and aerobic capacity (p< 0.05) related to physical fitness. In conclusion, interdisciplinary educational programmes based on the promotion of physical activity and life skills could contribute to the development of responsible daily physical activity habits in students to facilitate their transfer to other environments (social and family) outside school.