Several studies support the assumption that the brain-derived neurotrophic factor (BDNF) plays an important role in the pathophysiology of eating disorders. In the present cross-sectional and longitudinal study, we investigated BDNF levels in patients with anorexia nervosa (AN) at different stages of their illness and the association with cognitive functioning. We measured serum BDNF in 72 acutely underweight female AN patients (acAN), 23 female AN patients who successfully recovered from their illness (recAN), and 52 healthy control women (HCW). Longitudinally, 30 acAN patients were reassessed after short-term weight gain. The association between BDNF levels and psychomotor speed was investigated using the Trail Making Test.BDNF serum concentrations were significantly higher in recAN participants if compared to acAN patients and increased with short-term weight gain. In acAN patients, but not HCW, BDNF levels were inversely associated with psychomotor speed. AcAN patients with higher BDNF levels also had lower life time body mass indexes.Taken together, our results indicate that serum BDNF levels in patients with AN vary with the stage of illness. Based on the pleiotropic functions of BDNF, changing levels of this neurotrophin may have different context-dependent effects, one of which may be the modulation of cognitive functioning in acutely underweight patients.