The aim of the present study was to examine the associations of cardiovascular fitness (CVF) with a clustering of metabolic risk factors in children, and to examine whether there is a CVF level associated with a low metabolic risk. CVF was estimated by a maximal ergometer bike test on 873 randomly selected children from Sweden and Estonia. Additional measured outcomes included fasting insulin, glucose, triglycerides, HDLC, blood pressure, and the sum of five skinfolds. A metabolic risk score was computed as the mean of the standardized outcomes scores. A risk score <75th percentile was considered to indicate a low metabolic risk. CVF was negatively associated with clustering of metabolic risk factors in children. Receiver operating characteristic curve analysis showed a significant discriminatory accuracy of CVF in identifying the low/high metabolic risk in girls and boys (p < 0.001). The CVF level for a low metabolic risk was 37.0 and 42.1 mL/kg/min in girls and boys, respectively. These levels are similar to the health-related threshold values of CVF suggested by worldwide recognized organizations. In conclusion, the results suggest a hypothetical CVF level for having a low metabolic risk, which should be further tested in longitudinal and/or intervention studies.