Isolated rapid eye movement sleep behavior disorder (iRBD) is a harbinger for developing clinical synucleinopathies. Magnetic resonance imaging (MRI) has been suggested as a tool for understanding the brain bases of iRBD and its evolution. This review systematically analyzed original full text articles on structural and functional MRI in patients with video-polysomnography-confirmed iRBD according to systematic procedures suggested by Reviews and Meta-analyses (PRISMA). The literature search was conducted via the PubMed database for articles related to structural and functional MRI in iRBD from 2000 to 2020. Investigations to date have been diverse in terms of methodology, but most agree that patients with iRBD have structural changes in deep gray matter nuclei, cortical gray matter atrophy, and disrupted functional connectivity within the basal ganglia, the cortico-striatal and cortico-cortical networks. Furthermore, there is evidence that MRI detects structural and functional brain changes associated with the motor and non-motor symptoms of iRBD. The current review highlights the need for larger multicenter and longitudinal studies, using complex approaches based on data-driven and unsupervised machine learning that will help to identify structural and functional patterns of brain degeneration. In turn, this may even allow for the prediction of subsequent phenoconversion from iRBD to the clinically defined synucleinopathies.