AbstractResting state functional MRI (fMRI) and functional connectivity are widely applied in humans to examine the role of brain networks in normal function and dysfunction. A similar approach can be taken in rodents, either to obtain translational measures in models of brain disorders or to more carefully examine the neurophysiological underpinnings of the networks. A protocol for resting state functional connectivity in the anesthetized rat, from animal setup to data acquisition to possible pipelines for data analysis, is described. © 2018 by John Wiley & Sons, Inc.