The purpose of this study was to investigate the tracking of clustered metabolic syndrome (MetS) risk factor taking into account fatness and aerobic fitness from childhood to adolescence in Japanese children. This cohort study included 113 participants (47 boys and 66 girls) who were measured for MetS risk factors at 10 years and 13 years of age. Clustered MetS risk factors (MetS risk score) were calculated from the total gender-specific values (zscores) of the following five parameters: waist to height ratio (W/H), predictedtriglycerides, high density lipoprotein cholesterol, and mean arterial pressure. The tracking coefficient of MetS risk score from childhood to adolescence was 0.647 (p < 0.001). Correlation coefficients of MetS risk scores (without W/H) between 10 and 13 years of age in the high W/H group (r = 0.713, p < 0.001) were higher than those in the low W/H group (r = 0.402, p < 0.01) In addition, correlation coefficients of MetS risk scores (without pV ・ O2peak) between 10 and 13 years of age in the low pV ・ O2peak (r = 0.630, p < 0.001) were higher than those in the high pV ・ O2peak (r = 0.452, p < 0.01). In conclusion, we found that MetS risk was stable from childhood to adolescence in Japanese children. Furthermore, our results show that both fatness and fitness are crucial for tracking MetS risk.