In bioluminescence imaging (BLI), the biochemical reaction between a substrate and enzyme triggers light emission upon convergence. Unlike fluorescence imaging, BLI does not require excitation. In this protocol, we utilize the high signal-to-background ratio of the reaction between luciferase and its substrate to study the exchange of molecules between blood and cerebrospinal fluid. We outline steps for skull window thinning, cisterna magna infusion, intravascular retro-orbital injection, and imaging. For complete details on the use and execution of this protocol, please refer to Møllgård et al. (2023).¹