One factor that affects learning in the school context is motivation, as it serves as the driving force behind for commitment and active participation in the training process to achieve its goals and objectives. In the case of physical education in the school setting, the motivation towards physical activity that children and adolescents acquire for life is greatly shaped by the experiences that are developed through the subject. The objective of the study was to analyze the motivation in physical education classes among schoolchildren according to grade and gender, in the Araucanía region of Chile. The study followed a quantitative, cross-sectional methodological approach. A total of 196 students participated: 83 from fourth grade (54 boys and 29 girls) and 113 from eighth grade (68 boys and 45 girls). The main results revealed statistically significant gender differences in the dimensions of intrinsic motivation (p = 0.001), identified regulation (p = 0.024), and introjected regulation (p = 0.011), all with moderate effect sizes. In the comparison of motivation according to grade level, no statistically significant differences were found, however, mean scores were higher among fourth-grade students, indicating that motivation toward physical education decreases as students progress through the school cycle. This information is important for reflecting on didactic innovations and implementing changes in the subject.