Background: The childhood obesity has led to a decrease in physical activity, which may have detrimental effects on overall well-being, including impairment in musculoskeletal flexibility. Joint flexibility, often known as range of motion, is and a component of muscular fitness that essential for performing daily tasks. Considering the major physiological changes that occurs during adolescence have substantial impact on long-term health, this study aimed to investigate the relationship between body mass index (BMI) and the flexibility of the trunk and hamstring muscles among school adolescents. Methods: A total of 143 school adolescents were recruited using a convenience sampling method. The participants’ body composition was measured using the BMI, while the flexibility of the trunk and hamstring muscles was evaluated using the fingertip-to-floor test and the sit-and-reach test, respectively. The Spearman’s correlation coefficient was utilised to examine the relationship between BMI and muscle flexibility. Results: Most of the participants (n = 64, 44.8%) were underweight, with a mean BMI of 20.2 ± 5.2 kg/m2. There were no significant correlations between BMI and muscle flexibility (trunk, p = 0.965; hamstring, p = 0.829). Additionally, there were significant differences between males and females in trunk flexibility (p = 0.04), but not in hamstring flexibility (p = 0.135). Conclusion: There was no association between BMI and muscle flexibility in this study However, male students demonstrate significantly greater trunk flexibility compared to their female peers.