This review aims to systematically analyze the effect of exercise on muscle MCT protein levels and mRNA expression of their respective genes, considering exercise intensity, and duration (single‐exercise session and training program) in humans and rodents, to observe whether both models offer aligned results. The review also aims to report methodological aspects that need to be improved in future studies. A systematic search was conducted in the PubMed and Web of Science databases, and the Preferred Reporting Items for Systematic review and Meta‐Analyses (PRISMA) checklist was followed. After applying inclusion and exclusion criteria, 41 studies were included and evaluated using the Cochrane collaboration tool for risk of bias assessment. The main findings indicate that exercise is a powerful stimulus to increase MCT1 protein content in human muscle. MCT4 protein level increases can also be observed after a training program, although its responsiveness is lower compared to MCT1. Both transporters seem to change independently of exercise intensity, but the responses that occur with each intensity and each duration need to be better defined. The effect of exercise on muscle mRNA results is less defined, and more research is needed especially in humans. Moreover, results in rodents only agree with human results on the effect of a training program on MCT1 protein levels, indicating increases in both. Finally, we addressed important and feasible methodological aspects to improve the design of future studies.