Lower resting energy expenditure (REE) may partially explain the disproportionate prevalence of overweight/obesity among black African women. As no previous studies have investigated the REE of Southern African (South. Afr.) children, we aimed to determine, by sex and population group, the REE of 6- to 9-year-old urban school children. In a cross-sectional study with quota sampling, REE was measured with indirect calorimetry (IC). Confounders considered were: body composition (BC) (fat-free mass (FFM), FFM index, fat mass (FM), FM index), assessed using multifrequency bioelectrical impedance analysis, and physical activity (PA) measured with a pedometer. Multivariate regression was used to calculate REE adjusted for phenotypes (BC, z-scores of weight-for-age, height-for-age, body mass index-for-age) and PA. Sex and population differences in REE were determined with two-way ANOVA. Ninety-four healthy children (59.6% girls; 52.1% black) with similar socioeconomic status and PA opportunities participated. Despite BC variations, sex differences in REE were not significant (41 kcal/day; P = 0.375). The REE of black participants was lower than of white (146 kcal/day; P = 0.002). When adjusted for FFM and HFA z-score, the differences in REE declined but remained clinically meaningful at 91 kcal/day (P = 0.039) and 82 kcal/day (P = 0.108), respectively. We recommend the development of population-specific REE prediction equations for South. Afr. children.