Transcranial magnetic stimulation (TMS) is a widely used non-invasive technique in research and clinical settings. Despite its success, the cellular and molecular mechanisms underlying TMS-induced changes in the brain remain incompletely understood. Current protocols are largely heuristic, based on system-level observations. This study employed in vitro repetitive magnetic stimulation (rMS) in mouse brain tissue cultures, combined with computational modeling to develop an experimentally validated approach for predicting TMS effects. Unlike electrical or optogenetic stimulation, rTMS uniquely enhances plasticity by activating both pre- and postsynaptic neurons, with brain-derived neurotrophic factor (BDNF) playing a crucial role. Our simulations accurately predicted the frequency-dependent effects of rTMS, providing a critical step towards developing robust, validated tools that will enhance the precision and effectiveness of TMS applications across both research and clinical settings.