INTRODUCTION Multicomponent exercise programs have demonstrated benefits for both cognitive and physical function. However, their effects on brain-derived neurotrophic factor (BDNF) levels remain inconsistent, particularly in protocols incorporating functional exercises. This study aimed to evaluate the impact of two distinct multicomponent exercise protocols on BDNF levels and physical fitness in older women. METHODS Ninety physically active. community-dwelling older women (70.4 ± 7.2 years) were allocated to three different groups: 1) Multicomponent program 1: Circuit-based functional training; 2) Multicomponent program 2: Pilates Method; and 3) control group that received only health education. Both multicomponent programs were conducted over a 12-week period, with 50-minute sessions held three times per week. The control group participated in 12-week Health Education intervention with 90-minute sessions once a week. Brain-derived neurotrophic factor levels, short physical performance battery, agility, six-minute walk, and handgrip tests were measured. RESULTS Brain-derived neurotrophic factor levels increased significantly in both the functional training group (p<0.001) and Pilates group (p=0.005), with a more pronounced increase observed in the functional training group. The distance covered in the six-minute walk test also increased significantly in the functional training group (p=0.001) and was greater compared to both the Pilates (p<0.001) and control (p<0.001) groups. CONCLUSIONS Both multicomponent exercise programs led to increased BDNF levels after 12-week intervention. However, functional training yielded superior results compared to the Pilates method, possibly mediated by improvement in physical function.