Muscle functional magnetic resonance imaging (mfMRI) is an innovative technique that offers a noninvasive method to quantify changes in muscle physiology following the performance of exercise. The mfMRI technique is based on signal intensity changes due to increases in the relaxation time of tissue water. In contemporary practice, mfMRI has proven to be an excellent tool for assessing the extent of muscle activation following the performance of a task and for the evaluation of neuromuscular adaptations as a result of therapeutic interventions. This article focuses on the underlying mechanisms and methods of mfMRI, discusses the validity and advantages of the method, and provides an overview of studies in which mfMRI is used to evaluate the effect of exercise and exercise training on muscle activity in both experimental and clinical studies.