The effects of physical exercise on mental health have been extensively investigated, mainly in older people. Recent studies have looked into the acute effect of exercise on the brain using standardized low-resolution brain electromagnetic tomography (sLORETA). We assessed EEG power and mood changes after 20 min of aerobic exercise in elderly (N = 10) and young (N = 19) healthy individuals. Both groups showed improvement in total mood disturbance (TMD) post exercise (young: P = 0.03; elderly: P = 0.02). Only the young group showed significant improvement in anger (P = 0.05) and vigor (P = 0.006). Comparison pre versus post-exercise for each group separately revealed significant changes in the young group (an increase in alpha, beta-1 and beta-2 activity in Brodmann areas 24, 33 and 23, respectively). However, the elderly group did not show significant changes. An inverse correlation was found between alpha asymmetry and STAI (rs = -0.50; P = 0.029) in the young group. On the other hand, a significant correlation between beta-1 activity and TMD was observed in the elderly group (rs = 0.67; P = 0.045). We conclude that acute exercise can have distinct effects on brain activity and mood variables in young individuals when compared with elderly adults. However, additional studies are necessary to further investigate the role of exercise intensity in these results.