Objective: This study investigated the role of cognitive flexibility and temperament as predictors of academic performance, in children in care and children from a community sample, longitudinally. Also, it examined the mediating role of child's temperament in the relationship between cognitive flexibility and academic performance, as well as between-group differences. Method: Participants were 46 children in care and 48 children from a community sample, aged 6 to 10 years. Cognitive flexibility, temperament, and academic performance were assessed with the Raven's Colored Progressive Matrices set B (RCPM-B), the Portuguese version of School-Age Temperament Inventory (SATI), and the competence academic scale (CAS) of the Portuguese version of the Social Skills Rating System -- Teacher Form (SSRS-T), respectively. Results: Cognitive flexibility was a significant predictor of academic performance only for children in care. In both groups, negative reactivity and task persistence predicted academic performance, and children's task persistence mediated the relationship between cognitive flexibility and academic performance. However, a between group difference was observed in this mediation: in addition to the mediation effect observed in both groups, a direct effect was also found in the in-care group. Conclusions: These findings highlight the importance of promoting cognitive and task persistence competencies in normative and at-risk populations.