The purpose of the study was to model the relationships between intrinsic motivation, emotional intelligence and self-regulation of learning in physical education (PE) classes. The sample consisted on 480 students (248 boys and 232 girls) enrolled in year four of Primary Education (M = 9,29, DT = 0,52) from a total of 23 classes. Multilevel analysis taking intrinsic motivation as a dependent variable, revealed a statistically significant effect for school, planning, self-cheking, effort, regulation, emotional control and emotional recognition. The reduction in the intraclass correlation coefficient, from the null model to the final model, was approximately 67%. Promoting the development of emotional intelligence and improving self-regulation in PE classes could increase students' intrinsic motivation for this subject.