The estimation of body fat percentage (%BF) from anthropometry-related data requires population-specific equations to avoid incorrect interpretations in young athletes. Waist girth (WG) has been described as potential predictor of fat mass (FM) in several populations; however, there are no valid WG-based equations to estimate body composition in young Colombian athletes. The aim of this STandardisierte BerichtsROutine für Sekundärdaten Analysen STROSA-based study was twofold: i) to validate the relative fat mass (RFM) and its pediatric version (RFMp) compared to dual-energy x-ray absorptiometry (DXA) and ii) to develop a new equation (F20CA) to estimate the fat mass in Colombian children and adolescent elite athletes. A total of 114 young athletes that belong to the ‘Team Medellín’ program (58F, 56M; 51 children, 63 adolescents; 14.85 [2.38] years; 55.09 [12.16] kg; 162.38 [11.53] cm) participated in this cross-sectional study. The statistical analysis revealed a poor correlation, agreement and concordance of RFMp and RFM estimations with DXA measurements. After model specification using both Ordinary Least Square method and Bayesian analysis, the regression output revealed that sex, body mass-to-waist ratio, and waist-to-stature ratio were the statistically significant predictor variables that account for variability in FM. The new F20CA equation is expressed as FM (kg) = 5.46 ∗ (Sex) + 0.21 ∗ (BM/W [kg/m]) + 81.7 ∗ (W/Stature [cm/cm]) − 41.8 (R2 = 0.683; SEE = 2.468 kg), where sex is 0 for males and 1 for females. A moderate-to-high correlation and agreement of the F20CA was confirmed within the internal validation data set (R2 = 0.689; ICC [95%CI] = 0.805 [0.615, 0.904]; RMSE = 2.613 kg). The Bland–Altman analysis corroborated the high concordance between the reference method (DXA) and the F20CA-estimated FM (bias [95% LoA] = 1.02 [−3.77, 5.81] kg), indicating the two methods could be considered interchangeable. Even though external validation is needed, practitioners are advised to use the F20CA in young Colombian athletes with similar characteristics to those who participated in this study.