The latest evidence findings from exercise and cognition research support the benefits of physical exercise on children's and youths' cognition, proving that physical activity (PA), fitness and sport are positively associated with cognitive parameters of students' classroom behaviour and academic performance (AP). The majority of studies and intervention programs recognize cognition as a moderator between exercise and academic achievement, which involves a number of underlying mental processes such as cognitive (i.e. attention and memory) as well as executive functions. The cognitive functions are deemed as prerequisites of self-control, behavioural adaptability and academic achievement and thus remain at the focus of educational research. Until nowadays, the majority of exercise-cognition studies have been based mainly on a quantitative-medical model, since researchers have examined the relationship between exercise and academic performance under a dose-response perspective and with the purpose of prescribing physical exercise and activity guidelines. However, recent research brought into light the significance of the "contextual-interference effect hypothesis" on motor skill practice, or otherwise the importance of testing the influence of the training environment on motor skill learning. As a result, researchers have started to examine the qualitative characteristics of exercise and particular the different levels of coordinative and cognitive task complexity, along with their impact on students' cognition, academic behaviours and achievement. Given this growing interest in the relationship between exercise type and students' AP, the aim of the present paper is to synthesize and present the findings of the scientific literature that has examined this relationship in qualitative terms, within school-based PA intervention programs. By using both PA and AP as related search terms, a review of research articles was conducted, including studies from school-based physical activity contexts, such as physical education, recess, and extracurricular PA. Results from the review confirm the hypothesis that the combination of mentally challenging and socially engaging gross-motor and cognitive tasks, within PA programs, promote students' concentration, attention and classroom behaviour, while fostering their ability to use skills and knowledge. Given the increase in children's and youth's health-risk behaviours (violence, substance use, sedentary lifestyle), the present review findings could be used by educators or policy makers as guidelines for the development of quality PA programs that keep students physically, cognitively, and affectively on the learning curve.