Classroom-based physical activity (PA) is gaining attention in terms of its potential to enhance children’s cognitive functions, but it remains unclear as to which specific modality of PA affects cognitive functions most. The aim of the study was to examine the effects of qualitatively different PA breaks on children’s cognitive outcomes. Children (N = 142) aged between 7 and 9 years were allocated to a 20-week classroom-based PA program, with either high physical exertion and high cognitive engagement (combo group), high physical exertion and low cognitive engagement (aerobic group), or low physical exertion and high cognitive engagement (cognition group). Executive functions (updating, inhibition, shifting) and academic achievement (mathematics, spelling, reading) were measured pre- and post-intervention. Results showed that the combo group profited the most displaying enhanced shifting and mathematic performance. The cognition group profited only in terms of enhanced mathematic performance, whereas the aerobic group remained unaffected. These results suggest that the inclusion of cognitively engaging PA breaks seem to be a promising way to enhance school children’s cognitive functions.