Objective: Physical activity (PA) may influence acute stress reactivity in children differently depending on their weight. This randomized controlled trial investigated the impact of acute PA and of BMI status (overweight/obese (OB/OW) and normal weight (NW) on stress reactivity. Method: 50 prepubertal children (24 OW/OB and 26 NW) were randomly assigned to the PA or sedentary arm (SED) for 30 min followed by a stress task. Salivary cortisol, blood pressure (BP), and heart rate (HR) were measured. Results: An interaction effect between the randomization arms and weight status on salivary cortisol was found after the stress task (p = 0.04). Cortisol increased in the SED, but not in the PA arm (p = 0.004 for differences in time course) of NW children. Time course did not differ between both arms in OW/OB children (p = 0.7). OW/OB SED children had a flat cortisol course, and levels were reduced compared to the NW SED or the OW/OB PA children (p ≤ 0.03). Systolic BP increased only in the SED arm (p = 0.01). HR was higher in the PA than in the SED arm during stress (p < 0.001) and showed different time courses (p = 0.006). Conclusion: PA impacted on acute stress reactivity and influenced stress reactivity differently in NW and OW/OB children.