This review is intended to point out the role played by motor skills proficiency in the academic achievement of typically and atypically developing pupils who are attending primary school. First, the interplay between motor and cognitive development will be presented. Next, the cognitive phenotype, not yet deeply investigated, of a neurodevelopmental condition associated with the atypical development of motor functions (known as Developmental Coordination Disorder) will be illustrated. Thus, the contribution of motor functions to academic learning and the impact of motor difficulties for pupils attending primary school will be discussed. In addition, the importance of developing observational tools to be used in educational settings and the need for effective interventions designed to empower motor functioning and academic achievement of atypically developing pupils with motor deficits will be highlighted. Finally, future directions within the educational agencies for the early detection of the atypically developing motor trajectories and their treatment will be traced.