Brain-derived neurotrophic factor (BDNF) is a noncovalently linked homodimer protein from the neurotrophic growth factor family. Although it is expressed throughout the brain, it is produced more intensively in the entorhinal cortex and hippocampus and can cross the blood-brain barrier in two directions easily. The aim of this study is to understand, for the first time, whether there is a relationship between febrile seizure (FS) and BDNF. The study included cases diagnosed with FS and febrile illness, of similar age, weight, and height, between 6months and 6years. Samples for serum BDNF measurement were taken within the first 24-48h of admission at the hospital and levels were measured using the commercial enzyme-linked immunosorbent assay kit and expressed in ng/mL. Eighty cases (40 FS, 40 febrile illness) were included in the study. The mean serum BDNF was found to be 6.7±2.4ng/mL in the FS group and 4.5±2.6ng/mL in the febrile illness group (P=0.001). No relation was found between gender, age, body weight, length, and platelet counts and serum BDNF levels. The optimal cut-off value for serum BDNF was found to be 5.2ng/mL (75% sensitivity, 62.5% specificity, AUC: 0.723) to distinguish between FS and febrile illness. Excluding demographic variables such as gender, age, weight, length, and platelet counts serum BDNF levels have increased in children with FS. Considering the hippocampal origin of FS, we can suggest that the pathophysiology of FS may be related to the BDNF.