Isotopic tracers can reveal insights into the temporal nature of metabolism and track the fate of ingested substrates. A common use of tracers is to assess aspects of human carbohydrate metabolism during exercise under various established models. The dilution model is used alongside intravenous infusion of tracers to assess carbohydrate appearance and disappearance rates in the circulation, which can be further delineated into exogenous and endogenous sources. The incorporation model can be used to estimate exogenous carbohydrate oxidation rates. Combining methods can provide insight into key factors regulating health and performance, such as muscle and liver glycogen utilization, and the underlying regulation of blood glucose homeostasis before, during, and after exercise. Obtaining accurate, quantifiable data from tracers, however, requires careful consideration of key methodological principles. These include appropriate standardization of pretrial diet, specific tracer choice, whether a background trial is necessary to correct expired breath CO2 enrichments, and if so, what the appropriate background trial should consist of. Researchers must also consider the intensity and pattern of exercise, and the type, amount, and frequency of feeding (if any). The rationale for these considerations is discussed, along with an experimental design checklist and equation list which aims to assist researchers in performing high-quality research on carbohydrate metabolism during exercise using isotopic tracer methods.