Functional magnetic resonance imaging (fMRI) in mouse brain, paired with spatially and temporally defined manipulations, offers a powerful tool to causally explain the effect of specific neuronal activity on brain network dynamics. Here, we present an optimized protocol to measure cell-type-specific contributions to changes in whole-brain dynamics in mice using optogenetics (opto)-fMRI. This protocol details the injection of ChR2-expressing AAV, the implantation of optical fiber, the steps to perform opto-BOLD (blood-oxygenation-level-dependent) fMRI recording, and data analysis. For complete details on the use and execution of this protocol, please refer to Grimm et al. (2021).