This 12-week study investigates the effects of resistance training with different set structures on the plasma levels of brain-derived neurotrophic factor (BDNF), nerve growth factor (NGF), and obesity-related markers in middle-aged Korean women with obesity. A total of 40 middle-aged women with obesity (mean age, 59.87 ± 2.80 years) were enrolled in this study; only 31 women were able to complete the 12-week exercise period. The participants were randomly divided into the following four groups: control (CON,n= 8), drop set system (Drop,n= 8), descending set system (Descend,n= 7), and ascending set system (Ascend,n= 8). Body composition was recorded, and blood samples were obtained and evaluated before and after the 12-week exercise period intervention. Two groups showed no significant differences in body weight, body fat percentage, and body mass index before and after the 12-week exercise period. However, significant differences were observed in the blood levels of BDNF, NGF, adiponectin, leptin, and glucagon-like peptide-1 (GLP-1). BDNF and NGF showed significant differences in both time and interaction effects. Post hoc analysis revealed that the Drop group had higher BDNF and NFG levels than those of the Ascend and CON groups, while there was a significant increase in the levels of these biomarkers in the Descend and Drop groups in the time comparison. Adiponectin levels also showed significant differences in both time and interaction effects. Post hoc analysis revealed that the Drop and Descend groups had higher adiponectin levels than those of the CON group. Leptin levels decreased significantly in the Descend and Drop groups over time. GLP-1 levels showed no significant differences between the groups; however, there were significant differences in both time and interaction effects. Post hoc analysis revealed that the Drop group had lower GLP-1 levels than those of the CON group. This study suggests that resistance training with different set structures can have varying effects on the blood levels of different biomarkers in middle-aged women with obesity. These findings have implications for exercise prescription, and may provide insights into the mechanisms underlying the beneficial outcomes of resistance training in middle-aged Korean women with obesity.