Post-puberty, bone mass displays clear sex-specific patterns. However, research has suggested that a sexual dimorphism in bone mass is evident in younger children and is likely attributable to differences in lean mass. Thus, we aimed to determine whether the association with both overall muscle mass and/or muscle strength was different between the sexes in a paediatric population. Participants were recruited as part of the Vitamin D in Pregnancy Study, Australia. There were 209/402 (52.3%) children at the 11-year follow-up, and 172 had complete data. Children were assessed for bone mineral content (BMC), bone mineral density (BMD) and lean mass by DXA (Lunar). Handgrip strength (kg) was measured using a dynamometer (JAMAR). Linear regression models were adjusted for height, weight, age and pubertal stage. In adjusted models, including both muscle strength and lean mass, the observed association differed between boys and girls. At the spine in boys, BMC and BMD were associated with muscle strength (β 0.34 [95%CI 0.09–0.59] and 0.008 [95%CI 0.003–0.014];​ respectively) but not total muscle mass. However, muscle mass was associated with BMC and BMD at the total body (less head). In girls, spine BMC and BMD were associated with total lean mass (β 0.95 [95%CI 0.61–1.3] and β 0.01 [95%CI 0.005–0.02], respectively), with a similar pattern of association with total body (less head) measures. Muscle mass and strength appear to have sexually dimorphic effects on bone mass in school-aged children. These findings should be replicated in longitudinal studies.