Physical activity (PA) is well-documented to benefit students' executive function (EF) and academic performance. However, prevailing research has predominantly focused on domain-general EF (across academic domains) while overlooking domain-specific EF (within specific subjects). To address this gap, this opinion article proposes an integrative framework uniting domain-general and domain-specific EF to illuminate the cognitive mechanisms linking PA with academic achievement. Drawing on hierarchical and parallel models of EF interaction, this synthesis highlights how PA interventions can simultaneously strengthen broad self-regulatory skills and specialized cognitive processes to offer a complementary pathway to academic success. The opinion article also synthesizes emerging evidence that PA interventions enhance both broad EF capacities and targeted domain-specific skills (e.g., math-related working memory), offering dual pathways to improved academic outcomes. Accordingly, we propose a research agenda integrating psychometrically validated behavioral and neuroimaging assessments to capture domain-general and domain-specific EF, alongside multidimensional mediation and moderation models to clarify contextual influences (e.g., age, and socioeconomic status). Longitudinal PA interventions targeting both EF types are recommended to optimize cognitive and academic outcomes to inform evidence-based educational strategies.