OBJECTIVES: To investigate whether a single session of aerobic exercise improves inhibitory control in preadolescent children and whether this effect is mediated by changes in parasympathetic activity. DESIGN: In this experimental study, an intervention and control group were pair-matched by age, sex and moderate-to-vigorous physical activity. METHOD: 114 participants either completed a 20 min moderately-intense exercise bout on a cycling ergometer or watched a 20 min video. Prior to and after these conditions, a computer-based Stroop task was administered. During the cognitive task, heart rate variability (HRV) was measured using electrocardiography. RESULTS: Path-analyses did not support an association between group and posttest accuracy on the Stroop task, while controlling for pretest scores. However, the intervention group had lower time-domain based HRV at posttest. The examination of mediation models revealed a moderation by sex, as the relation of lower time-domain based HRV with higher accuracy on both congruent and incongruent trials of the Stroop task was observed in girls only. CONCLUSION: A single aerobic exercise session does not necessarily improve inhibitory control in preadolescent children. However, the manipulation of the autonomic state towards a parasympathetic withdrawal has the potential to alter inhibitory control in girls in particular.