In multiple sclerosis (MS), physical and cognitive deficits not only reflect structural damage, but also functional imbalance in and between brain networks. Resting-state functional magnetic resonance imaging (fMRI) allows one to investigate intrinsic, synchronized brain activity across the whole brain, and to measure the degree of functional correlation between different cortical regions. This review describes the major findings obtained in MS patients at different clinical stages using resting state fMRI, and discusses how the use of fMRI techniques may improve our ability to identify novel biomarkers useful in the context of the diagnostic work-up, establishing prognosis and monitoring treatment.