Executive functions and metacognition are two cognitive predictors with well-established connections to academic performance. Despite sharing several theoretical characteristics, their overlap or independence concerning multiple academic outcomes remain under-researched. To address this gap, the present study applies a latent-variable approach to test a novel theoretical model that delineates the structural link between executive functions, metacognition, and academic outcomes. In whole-class sessions, 469 children aged 9 to 14 years (M = 11.93; SD = 0.92) completed four computerized executive function tasks (inhibition, working memory, cognitive flexibility, and planning), a self-reported metacognitive monitoring questionnaire, and three standardized tests of academic ability. The results suggest that executive functions and metacognitive monitoring are not interchangeable in the educational context and that they have both shared and unique contributions to diverse academic outcomes. The findings are important for elucidating the role between two domain-general cognitive skills (executive functions and metacognition) and domain-specific academic skills.