Normal-weight obesity (NWO) syndrome has been shown to be associated with cardiometabolic dysfunction. However, little is known regarding this potential relationship in Latin American children and adolescents. The aim of this study was two-fold: (i) to investigate whether Colombian youth with NWO syndrome have a poorer cardiometabolic profile and physical fitness performance than normal-weight lean (NWL) peers; and (ii) to determine if physical fitness levels are related to prevalence of normal-weight obesity in youth. This was an analytical cross-sectional study of 1919 youths (9–179 years old, 53.0% girls) in the capital area of Colombia. NWO was defined as a body mass index < 25 kg/m2 and a validated body fat percentage above the sex-age-specific 90th percentile for Colombian children and adolescents. Body fat was estimated using bioelectrical impedance analysis, cardiorespiratory fitness (CRF) was estimated using the 20-meter shuttle run test, and muscular fitness with the handgrip test. Biochemical profile blood samples were collected for cardiometabolic risk factors. After adjusting for chronological age, pubertal stage, and Mediterranean diet adherence, the NWO group (boys and girls) had significantly higher values for cardiometabolic risk factors, and waist circumference (WC) than the NWL group. The prevalence of NWO was lower in youth classified with healthy CRF (boys, odds ratio (OR) = 0.54, 95% confidence interval (CI) 0.37 to 0.78; girls, OR = 0.35, 95% CI 0.24 to 0.50), p < 0.001. Our findings indicate that using only body mass index for the assessment of cardiometabolic risk likely misrepresents true adiposity and suggest the need to include the assessment of body fat in the routine clinical evaluation of individuals during childhood and adolescence.