Background: The purpose of this study was to investigate the effects of a 16-week exercise program combining aerobic and resistance training on body composition, growth differentiation factor-15 (GDF-15), apelin-12, and interleukin-15 (IL-15) in older Korean women according to obesity status. Methods: Participants were divided into obesity (n = 15) and normal-weight groups (n = 14). A walking exercise was performed at 60-70% heart rate reserve (RPE 13-15). The bodyweight resistance exercises were progressively intensified over 16 weeks. Analysis methods included two-way repeated measures ANOVA, ANCOVA, and paired and independent t-tests. Results: Significant main effects of time and group were observed in body weight (p < 0.001), and both groups demonstrated significant within-group reductions in body mass index (BMI) (obese: p < 0.001; normal-weight: p < 0.05), along with significant between-group differences (p < 0.001). The percentage of body fat significantly decreased over time (p < 0.01) and differed between groups (p < 0.001). GDF-15 exhibited a significant group × time interaction (p < 0.05) and a main group effect (p < 0.05). Although no statistically significant changes were observed in Apelin-12 levels, an opposite trend was identified between groups, with an increase in the obese group and a decrease in the normal-weight group. For IL-15, no significant interaction effect was found between the groups. Conclusions: The 16-week combined exercise intervention improved key markers of body composition, particularly in obese older women, and led to increased GDF-15, indicating potential metabolic benefits. While changes in apelin-12 and IL-15 were not statistically significant, the findings support the utility of combined exercise for mitigating fat accumulation and promoting healthy aging in older adults.