Exercise metabolism in children has traditionally been assessed using the respiratory exchange ratio (RER) to determine the contributions of fat and carbohydrate to the exercise energy demands. Although easily measured, RER measurements have limitations. Other methods to assess metabolism such as the obtainment of a muscle biopsy and the use of nuclear magnetic resonance spectroscopy carry ethical and feasibility concerns, respectively, which limit their use in studies involving children. Stable isotopes, used routinely in studies involving adults, can also be applied in studies involving children in an ethical and feasible manner. Two common stable isotopes used in metabolic studies involving children include carbon-13 (¹³C) and nitrogen-15 (¹⁵N). ¹³C-glucose can be used to study carbohydrate metabolism and ¹⁵N-glycine can be used to assess protein metabolism. This article reviews the use of ¹³C-glucose and ¹⁵N-glycine to study exercise metabolism in children, considers some of the associated ethical aspects, explains the general methodology involved in administering these isotopes and the resources required, and describes studies involving children utilizing these methods. Finally, suggestions for future research are provided to encourage further use of these techniques.