Brain-derived neurotrophic factor (BDNF) is a factor that implicate in the pathophysiology and treatment of depression and anxiety. The aim of this study was to determine the relationship between dental anxiety and BDNF serum level through impacted third molar surgery. In this randomized, double-blind, cross-sectional study, the sample included patients who had been admitted for the impacted third molar extraction under local anesthesia between January to November 2020. The primary predictor variable was serum BDNF level and the second predictor variable was dental anxiety scores before and after operation in patients. The primary outcome variable was the correlation between anxiety scores (APAIS, MDAS, STAI, VAS) and serum BDNF level. The sample included 55 patients (22 Male, 33 Female) aged 18 to 42 (24,2+5,55). Comparison of pre-operative scores (APAIS, MDAS, STAI, VAS and BDNF) and post-operative scores were statistically significant (P < .05). Post-operatively, MDAS and VAS scores decreased, while BDNF levels and STAI scores increased compared to the preoperative scores. BDNF was not correlated with APAIS, MDAS, STAI, and VAS preoperatively and postoperatively. There may be a relationship between serum BDNF level and dental anxiety scale, but, no correlation was found between them.