Transcranial magnetic stimulation (TMS) is a non-invasive brain stimulation technique for modulating neocortical excitability in humans. Repetitive magnetic stimulations (rMS) applied to tissue cultures trigger functional changes of dendritic spines alongside a potentiation of excitatory neurotransmission. Furthermore, in vivo studies involving both animal models and patients have demonstrated the therapeutic potential of rTMS in treating psychiatric disorders.Despite its use in both neuroscience research and clinical settings, the molecular mechanisms of rTMS-based interventions remain not well understood. Specifically, the role of microglia in mediating rTMS effects has not been thoroughly explored.In this study, we investigated the impact of intermittent theta burst stimulation (iTBS) — consisting of 900 pulses administered daily over ten days — on organotypic brain tissue cultures from mice. Electrophysiological recordings revealed a decrease in the frequencies of AMPA-receptor-mediated spontaneous excitatory postsynaptic currents following rTMS-iTBS intervention. Live imaging experiments further showed a reduction in microglial process motility. Moreover, rTMS-iTBS led to a decrease in markers indicative of reactive microglia, including CD68 expression and IFN-gamma.These findings suggest that rTMS-iTBS could offer therapeutic potential for conditions characterized by neuronal hyperexcitability and microglial hyper-reactivity.