Introduction: Physical activity performed in the school context plays an important role in the physical and psychological well-being of children and adolescents. Objective: To evaluate the effect of a comprehensive physical activity program based on modified games and healthy habits on the physical fitness of school children in an educational institution. Methodology: Quasi-experimental study with pre-test-post-test design in an experimental group (GEX) (35 total; 23 boys, 12 girls, 11.4±0.7 years), and a control group (GC) (33 total, 17 boys and 16 girls, 11.7±0.6 years). The intervention lasted 14 weeks. Pre- and post-intervention physical fitness tests were administered. Physical activity (PA) and screen time (PT) were measured through pre-questions of the youth activity profile questionnaire (YAP-S). Discussion: Physical activity interventions in school can have a small to moderate effect on physical fitness in both children and adolescents. On the other hand, interventions that use games produce improvements in children's and adolescents' enjoyment. Conclusions: A physical activity and healthy habits intervention program showed effects attributable to the intervention on flexibility and screen time. In addition, the program generated greater enjoyment of PA and physical education classes.