Mouse optogenetic functional magnetic resonance imaging (opto-fMRI) is critical for linking genes and functions and for mapping cell-type-specific neural circuits in the whole brain. Herein, we describe how opto-fMRI images can be reliably obtained in anesthetized mice with minimal distortions at ultrahigh magnetic fields. The protocol includes surgical and anesthesia procedures, animal cradle modification, animal preparation and setup, animal physiology maintenance, and pilot fMRI scanning. This protocol will enable reproducible mouse opto-fMRI experiments. For complete details on the use and execution of this protocol, please refer to Jung et al. (2021), Jung et al. (2022), and Moon et al. (2021)..