Low levels of brain derived-neurotrophic factor (BDNF) and excessive screen exposure are risk factors for neurocognitive deficits and obesity in youth, but the relationship between screen time and BDNF remains unknown. This study examined whether duration and/or type of sedentary screen time behaviour (TV viewing, video games, recreational computer use) are associated with serum BDNF levels in youth with obesity. The sample consisted of 250 inactive, postpubertal adolescents with obesity (172 females/78 males, aged 15.5 ± 1.4 years) at the baseline assessment of the Healthy Eating, Aerobic, Resistance Training in Youth Study. After controlling for self-reported age, sex, race, parental education, puberty stage, physical activity, and diet, higher total screen exposure was significantly associated with lower serum BDNF levels (β = −0.21, p = 0.002). TV viewing was the only type of screen behaviour that was associated with BDNF levels (β = −0.22, p = 0.001). Higher exposure to traditional forms of screen time was independently associated with lower serum BDNF levels, and this association appears to be driven primarily by TV viewing. Future intervention research is needed to determine whether limiting screen time is an effective way to increase BDNF and associated health benefits in a high-risk population of youth with obesity. Trial Registration: ClinicalTrials.Gov NCT00195858.