Background: Optimal bone health is vital in children to prevent osteoporosis later in life, and body composition plays a crucial role in it. However, the literature reports contradictory results when considering the relationship between body composition and bone health in children. This study aimed to examine the bone health and its relationship with body composition in Malaysian schoolchildren. Methods: In this cross sectional study, body composition data (weight, height, body fat percentage [% fat], fat mass, fat free mass, visceral fat, waist circumference [WC] and body mass index-for-age [BMI z-score]) and bone health data (Z-score and broadband ultrasound attenuation [BUA]) were collected from 415 schoolchildren aged 9–12 years, cluster sampled from randomly selected primary schools in Kuala Lumpur, Malaysia. Results: Girls generally had significantly higher height, body fat percentage, fat mass, visceral fat and Z-score as compared to boys. A steady increase of the mean BUA value was observed with increasing age in both sexes. The mean BUA value of the present study across the population was significantly higher than that of schoolchildren from Nigeria (p < 0.001), Colombia (p < 0.001) and Spain (p = 0.002). Significant positive correlations were found between all the body composition variables and bone outcome variables across the population. Further, BUA was significantly correlated with weight (β = 0.172; p = 0.001), height (β = 0.299; p < 0.001), % fat (β = 0.131; p = 0.007), fat mass (β = 0.130; p = 0.007), fat free mass (β = 0.209; p < 0.001), visceral fat (β = 0.127, p = 0.008), WC (β = 0.165; p = 0.001) and BMI z-score (β = 0.162; p = 0.001), after controlling for sex, age and ethnicity. Similarly, after confounders adjusted, Z-score was significantly predicted by weight (β = 0.160; p = 0.001), height (β = 0.310; p < 0.001), % fat (β = 0.104; p = 0.032), fat mass (β = 0.107; p = 0.026), fat free mass (β = 0.218; p < 0.001), visceral fat (β = 0.107, p = 0.026), WC (β = 0.145; p = 0.002) and BMI z-score (β = 0.150; p = 0.002). Conclusions: Our findings have revealed that body composition variables were positive correlated with bone outcome variables, suggesting that adipose tissue acts to stimulate bone growth. Further clinical and molecular studies in the future is recommended to fully illustrate the complex interactions between adiposity and bone health.