Purpose Insulin resistance may exert a negative influence on bone mass in childhood and adolescence. The objective was to assess the association between insulin resistance and total body less head (TBLH) bone mineral content (BMC) and to investigate whether body composition, physical activity or osteocalcin levels may influence this association. Methods A longitudinal study with follow-up over more than 6 years was performed and included 562 apparently healthy participants with a mean age of 9.6 years at baseline. Participants underwent DXA scanning at baseline. At the two follow-ups, participants had performed another DXA scanning, had blood samples taken for fasting insulin, glucose and osteocalcin and had physical activity measured with an accelerometer. HOMA-IR was calculated as an index of insulin resistance. Results HOMA-IR was negatively associated with TBLH BMC in boys at follow-ups (β = −31.4, p < 0.001) after adjustment for maturity, height, bone area, and baseline level of TBLH BMC. The negative association remained almost unchanged after further adjustments for body composition and physical activity. No association between HOMA-IR and TBLH BMC was found in girls. Conclusion Insulin resistance may be detrimental for bone development through puberty in boys independent of body composition and the level of physical activity.