Acute exercise has been found to reduce subsequent energy intake in obese adolescents. Although it has been suggested that some neural pathways are involved in this post-exercise energy intake regulation, it remains unknown whether the post-exercise attentional response to food cues differs as a function of weight status. We hypothesize that there will be a reduction in the neural response to food cues as a result of exercise in obese adolescents, but not in their lean counterparts. Fourteen obese and 14 lean adolescent boys (12–15 years) were randomized (within-subjects design) to remain seated (CON) or to exercise 45 minutes at 65% of their maximal capacities (EX). After the exercise or sitting period, the adolescents' cognitive engagement in the processing of food vs. non-food cues was assessed during an attentional computer-based task with electroencephalography (EEG) recording. An ad libitum lunch meal was offered and appetite feelings were assessed (visual analog scales). There was no main effect of condition on energy intake in lean subjects, but obese adolescents ate significantly less following EX compared with CON (P < .05). There was no effect of condition or stimulus type (food vs. non-food) on the EEG-recorded amplitude of the P3b component in lean adolescents. However, the response to food cues was significantly reduced compared with non-food stimuli after exercise in obese participants (P < .01). Following EX, but not CON, total body weight, body mass index, and fat mass were inversely correlated with the EEG response to food–non-food stimuli (all P < .05). However, this response was not associated with ad libitum EI (both P > .1). Acute exercise favors decreased neural response to food cues compared with non-food cues in obese but not lean adolescents, suggesting differential effects of exercise on the neural processing of food cues based on weight status.