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We previously showed that exposing mice to visual flickering stimulation increased mitogen activated protein kinase and nuclear factor kappa-light-chain-enhancer of activated B cells signaling in the visual cortex (VC) in a manner dependent on the duration and frequency of stimulation. Because these pathways control multiple neuronal and glial functions, here we aimed to define the transcriptional effects of different frequencies and durations of audiovisual flicker (AV flicker) stimulation on multiple brain functions. Within the VC, we found that all stimulation frequencies caused fast activation of a module of immune genes within 0.5\u2009h and slower suppression of synaptic genes after 4\u2009h. In the hippocampus, we found that a 20\u2009Hz AV flicker activated a module of genes associated with mitochondrial function, metabolism, and synaptic translation, while 10\u2009Hz rapidly suppressed a module of genes linked to neurotransmitter activity. 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