In this study, we explored the predictive role of behavioral measures of Executive Functions (EFs) and a self-report measure of Effortful Control (EC) on the academic performance of early adolescents. We also analyzed the mediating role of self-reported empathy and social behavior rated by peers (i.e., prosocial behavior and social preference) and by the lead teacher (i.e., social competence). A sample of 244 adolescents aged between 12 and 13 years participated in the study. The resulting structural equation model indicated that EFs and EC predict academic performance in a complementary and independent way. Results also confirmed the mediating role of empathy and social behavior. The final model explained 64% of academic performance. We discuss the appropriateness of obtaining complementary measures of EFs and EC in predictions of academic performance as well as the importance of introducing activities involving self-regulation, empathy, and socioemotional skills in the school setting.