The purpose of the present study was to examine the associations between physical fitness and body fatness with blood lipid profile in 231 Japanese children and adolescents (12.1 ± 1.5 years). The primary outcomes of the present study were a lipid risk score which was calculated by summing up z scores of three lipid items (triglycerides, low density lipoprotein-cholesterol, and high density lipoprotein-cholesterol). Physical fitness was assessed by using the Japanese standardised fitness test. For body fatness, a percentage of overweight was calculated with using age-, sex-, height-specific standardised body mass. For combined analysis (fitness × fatness), the participants were cross-tabulated into four groups (Non-Obese/Higher-Fit, Non-Obese/Lower-Fit, Obese/Higher-Fit, and Obese/Lower-Fit). The results demonstrated that the participants in fitness categories A/B [most fit] and C [middle] demonstrated the lower (better) lipid risk score than the participants in fitness categories D/E [least fit] (F _{(2, 222)} = 6.03, p = .003). For body fatness, the lipid risk score in obese group was significantly higher (worse) than that in thin and normal groups (F _{(2, 222)} = 6.08, p = .004). The combined analysis showed that there was a significant interaction (fitness × fatness) on the lipid risk score (F _{(1, 221)} = 4.05, p = .047), suggesting that Obese/Lower-Fit group had the worst risk score compared to the other groups. The present study suggests that improving both fitness and body fatness might be important for better lipid profile in Japanese children and adolescents.