Our purpose was to evaluate the effect of physically active lessons (PAL) on the cognitive performance of children during two years of follow-up. Four classes (second grade of elementary school) were divided into two intervention classes (n = 34) and two control classes (n = 27). Evaluations were performed before the intervention (M1), after 3 (M2) and 9 (M3) months in the 1st year, and 14 (M4) and 18 (M5) months in the 2nd year. The intervention was based on PAL integrated with the curricular components, which stimulated the children to stand or move in the classroom. Cognitive performance was evaluated using three computerized tests for response inhibition, selective attention, and cognitive flexibility. The children in the intervention classes presented improved cognitive performance in the execution of all tasks along the two years follow-up, in both correct answers and time reactions, with exception of correct answers of visual search. For the intervention classes, in most of the tasks, the mean differences confidence interval of 95% did not include the 0 on the two last moments of evaluation, and in all cases, the mean differences of them between M1 versus M5 were significantly different with high values of effect size (cohen -d > 1). PAL promotes modest improvements in diverse cognitive functions in children.