OBJECTIVE: The purpose of this study was to examine the associations between objectively measured physical activity and serum brain-derived neurotrophic factor (BDNF) in adolescents. METHODS: Cross-sectional analyses were performed using data from 415 adolescents who participated in the 2015 follow-up of the Childhood Health Activity and Motor Performance School Study Denmark (the CHAMPS-study DK). Physical activity was objectively measured by accelerometry monitors. Serum BDNF levels were analyzed using the Enzyme-linked immunosorbent assay (ELISA). Anthropometrics and pubertal status were measured using standardized procedures. RESULTS: With adjustment for age, pubertal status and body mass index, mean physical activity (counts per minute) was negatively associated with serum BDNF in boys (P=0.013). Similarly, moderate-to-vigorous physical activity (MVPA) was negatively associated with serum BDNF in boys (P=0.035). In girls, mean physical activity and MVPA were not associated with serum BDNF. Without adjustment for wear time, sedentary time was not associated with serum BDNF in either sex. CONCLUSION: These findings indicate that higher physical activity is associated with lower serum BDNF in boys, but not in girls.