Purpose Few studies have investigated the independent and joint associations of cardiorespiratory fitness (CRF) and body fat percentage (BF%) with insulin resistance in children. We investigated the independent and combined associations of CRF and BF% with fasting glycaemia and insulin resistance and their interactions with physical activity (PA) and sedentary time among 452 children aged 6–8 years. Methods We assessed CRF with a maximal cycle ergometer exercise test and used allometrically scaled maximal power output (Wmax) for lean body mass (LM1.13) and body mass (BM1) as measures of CRF. BF% and LM were measured by dual-energy X-ray absorptiometry, fasting glycaemia by fasting plasma glucose, and insulin resistance by fasting serum insulin and Homeostatic Model Assessment for Insulin Resistance (HOMA-IR). PA energy expenditure (PAEE), moderate-to-vigorous PA (MVPA), and sedentary time were assessed by combined movement and heart rate sensor. Results Wmax/LM1.13 was not associated with glucose (β=0.065, 95% CI=-0.031 to 0.161), insulin (β=-0.079, 95% CI=-0.172 to 0.015), or HOMA-IR (β=-0.065, 95% CI=-0.161 to 0.030). Wmax/BM1 was inversely associated with insulin (β=-0.289, 95% CI=-0.377 to -0.200) and HOMA-IR (β=-0.269, 95% CI=-0.359 to -0.180). BF% was directly associated with insulin (β=0.409, 95% CI=0.325 to 0.494) and HOMA-IR (β=0.390, 95% CI=0.304 to 0.475). Higher Wmax/BM1, but not Wmax/LM1.13, was associated with lower insulin and HOMA-IR in children with higher BF%. Children with higher BF% and who had lower levels of MVPA or higher levels of sedentary time had the highest insulin and HOMA-IR. Conclusion Children with higher BF% together with less MVPA or higher levels of sedentary time had the highest insulin and HOMA-IR. CRF appropriately controlled for body size and composition using LM was not related to insulin resistance among children.