This study examines the longitudinal agreement between waist circumference-to-height ratio (WHtR) and dual-energy X-ray absorptiometry (DEXA)-measured fat mass in 7237 children over a 15-year period. The results show that WHtR provides better longitudinal absolute agreement with DEXA-measured total fat mass and trunk fat mass compared to body mass index (BMI). Specifically, WHtR had a higher intraclass correlation (ICC) and area under the curve (AUC) for predicting excess total fat mass and trunk fat mass than BMI. The optimal WHtR cutpoints for predicting excess total fat mass were 0.50–0.53 in males and 0.52–0.54 in females. These findings suggest that WHtR is an inexpensive and accurate alternative to BMI for predicting fat mass in pediatrics, particularly in low-resource settings where more complex fat mass measures are not readily available. The study highlights the need to shift away from BMI as a proxy weight-for-height index, which can misidentify and misdiagnose pediatric obesity, towards more accurate assessments of fat mass.This study examines the longitudinal agreement between waist circumference-to-height ratio (WHtR) and dual-energy X-ray absorptiometry (DEXA)-measured fat mass in 7237 children over a 15-year period. The results show that WHtR provides better longitudinal absolute agreement with DEXA-measured total fat mass and trunk fat mass compared to body mass index (BMI). Specifically, WHtR had a higher intraclass correlation (ICC) and area under the curve (AUC) for predicting excess total fat mass and trunk fat mass than BMI. The optimal WHtR cutpoints for predicting excess total fat mass were 0.50–0.53 in males and 0.52–0.54 in females. These findings suggest that WHtR is an inexpensive and accurate alternative to BMI for predicting fat mass in pediatrics, particularly in low-resource settings where more complex fat mass measures are not readily available. The study highlights the need to shift away from BMI as a proxy weight-for-height index, which can misidentify and misdiagnose pediatric obesity, towards more accurate assessments of fat mass.