High accuracy in estimating energy expenditure is essential for enhancing sports performance. The resting metabolic rate (RMR), as a primary component of total energy expenditure (TEE), is commonly estimated using predictive equations. However, these references may not be applicable to adolescent athletes. The purpose of this cross-sectional study was to analyse the differences between predicted RMR in relation to energy expenditure measured by indirect calorimetry (IC) among 45 Brazilian male adolescent football athletes. Indirect calorimetry (IC) and anthropometric (bioimpedance) measurements were recorded at a single visit to the laboratory after fasting overnight. The mean age was 15.6 ± 1.14 years, body mass was 63.05 ± 7.8 kg, and height was 172 ± 7.5 cm. The RMR values predicted by equations proposed by the Food and Agriculture Organization (FAO) (United Nations), Henry and Rees (HR), Harris Benedict (HB), and Cunningham (CUN) were compared with IC RMR values, by correlation analysis. The FAO and HR predictive equations yielded different values from IC (IC: 1716.26 ± 202.58, HR: 1864.87 ± 147.78, FAO: 1854.28 ± 130.19, p = 0.001). A moderate correlation of 0.504 was found between the results of HB and IC. In the survival-agreement model, the CUN equation showed low disagreement with the IC RMR, with error values between 200 and 300 kcal/day. The results showed that HB and CUN yielded similar values as IC, with the CUN equation showing low disagreement with IC; hence, adolescent athletes should undergo evaluation with precise laboratory methods to ensure that accurate information about RMR is recorded.