Background: Endometriosis is an estrogen-dependent chronic progressive gynecological disease that affects around 10% of women of reproductive age. A recent study shows that brain-derived neurotrophic factor (BDNF) has the potential as a clinical marker in the diagnosis of endometriosis. We aimed to determine whether BDNF levels are correlated with pain scores associated with endometriosis. Methods: Fifty women who underwent laparoscopy surgery at Dr. Soetomo General Hospital and Dr. Ramelan Navy Hospital were prospectively recruited from October 2017 until August 2018. A blood sample was obtained before surgery and BDNF was measured using the Human BDNF Quantakine®️ kit. The relationship of BDNF levels in serum with the diseases's level of pain and stages was compared between cases and controls. BDNF validity as an endometriosis diagnosis biomarker was assessed using receiver operating characteristic (ROC) analysis. Results: Serum concentrations of BDNF were significantly greater in women with endometriosis (30.42±7.41 pg/ml), compared to controls (25.66±3.30 pg/ml). Serum concentrations of BDNF were moderately correlated with the patient’s reported pain scores (r=0.44, p=0.01). Receiver operating characteristic curve analysis confirmed the potential of BDNF in the diagnosis of endometriosis. Using a cut-off value of 27.06 pg/ml, the sensitivity and specificity were reported to be 66.7% and 64.3%, respectively. Conclusion: BDNF serum levels in endometriosis women are significantly higher than in women without the disorder. BDNF serum level seems to have low accuracy and predictive value as a diagnostic marker for endometriosis. However, there was a moderate relationship between BDNF serum level and the degree of pain.