Background Transcranial pulse stimulation (TPS) has recently been proposed as a promising non-invasive technique for treating neurological disorders. While neuropsychological improvements in treated Alzheimer's disease (AD) patients support its safety and preliminary clinical effectiveness, the fundamental mechanisms of TPS action on the brain remain unclear. Objective In this study, we explore the effects of TPS on neuronal activity and brain circuitry in healthy and AD mouse models. Methods We utilized fluorescence calcium imaging combined with resting-state functional magnetic resonance imaging and c-Fos immunohistochemistry for validation. We imaged TPS-treated mouse brains expressing genetically encoded calcium indicator and compared the imaging data from AD mouse strains to wild-type controls, followed by immunohistochemical analysis of neuronal activation to support the in vivo imaging findings. Results TPS induced robust calcium influxes in GCaMP + mice, increased c-Fos expression in the dentate gyrus, and rapidly but transiently reorganized functional connectivity across brain networks, particularly within the hypothalamus, hippocampus, and other limbic regions. At higher stimulation intensities, TPS is shown to trigger spreading depolarization waves. Conclusion These findings support the hypothesis that TPS-induced mechanical effects can effectively modulate brain activity while averting tissue heating and cavitation, thus shedding light on observed beneficial effects in patients and paving the way for further optimization of TPS as a therapeutic strategy for neurodegenerative diseases.