© 2019, © 2019 European College of Sport Science. Background: Brain-derived neurotrophic factor (BDNF) increases neuronal viability and cognitive function, peripheral lipid metabolism and skeletal muscle repair. The primary purpose of this study was to determine the effect of short-term high-intensity interval training (HIIT) on serum BDNF concentrations in healthy young women. Methods: Seventeen women (age:22 ± 1 years); body mass index (BMI:24.2 ± 2.2 kg/m²), body fat percentage (% fat:25.8 ± 4.7) participated in the study. Participants were randomly assigned to a control (n = 8) or HIIT group (n = 9). All participants performed a graded exercise test (GXT) on an electronically-braked cycle ergometer to determine maximal aerobic power (MAP, Watts). HIIT was performed three days per week for four weeks. Each HIIT session consisted of three to five cycling bouts of 30 s each at 80% MAP, followed by four-minutes of recovery at 40% MAP. Forty-eight hours after the last bout of exercise, both groups performed a follow-up GXT. Non-fasting blood samples were collected before and immediately after each GXT. Mixed factorial (2 groups x 4 measures, and 2 groups x 2 measures) ANOVA was used to assess BDNF concentrations, performance and anthropometric variables. Results: Serum BDNF concentrations in the HIIT group (21.9 ± 1.3 ng/mL) increased compared to control (19.2 ± 2.8 ng/mL) (∼12%, P < 0.05) following HIIT. In contrast, circulating BDNF concentrations were reduced following the GXT (P < 0.05). The MAP and % Fat did not change with HIIT. Conclusions: Twelve sessions of HIIT increases circulating BDNF concentrations in healthy young women despite no change in physical performance or % fat.