Physical activity has been shown to enhance circulating brain-derived neurotrophic factor (BDNF) in animals and humans. However, the exact time course and sex-specific modulation of peripheral BDNF in response to exercise are still poorly understood. We examined the kinetics of BDNF serum concentrations in response to perceived high-intensity and low-intensity exercise, and during a subsequent recovery period by taking several blood samples during each phase. Furthermore, we compared the BDNF concentration between young men and women taking oral contraceptives. We found transient BDNF elevations during physical activity only for the high-intensity condition. Here, BDNF reached its maximum serum concentration after 20 min of exercise, and returned to baseline after approximately 10 min of recovery. Although there were no sex differences during baseline or recovery, the increase in the BDNF concentration during the exercise phase was more pronounced in men than in women.