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Body fat mass (FM) has advantages over body mass index (BMI) in terms of accuracy of fitness assessment and health monitoring. However, the relationship between FM and fitness in Chinese children has not yet been well studied. This study aimed to investigate the relationship between health-related physical fitness, BMI, and FM, which was estimated using a predictive model among elementary schoolchildren in China. This cross-sectional study included 2677 participants (boys, 53.6%; girls, 46.4%) who underwent anthropometric measurements (height, weight, BMI, and FM) and five health-related fitness tests: 50-m sprint (speed), sit and reach (flexibility), timed rope-skipping (coordination), timed sit-ups (muscular endurance), and 50-m × 8 shuttle run (endurance). In boys, BMI showed a positive correlation with speed (p < 0.001) and endurance (p < 0.006) tests and a negative correlation with flexibility (p < 0.004) and coordination (p < 0.001) tests. In girls, a positive correlation between speed (p < 0.001) and endurance (p < 0.036) tests was observed. Both BMI and FM (estimated using the predictive model) were strongly associated with the health-related physical fitness of elementary schoolchildren. Our findings indicate that health-related physical fitness was similarly affected by FM and BMI. As FM can be quantified, it could therefore be used to develop strategies and intervention programs for the prevention and management of obesity in children.