Background <p>Repetitive transcranial magnetic stimulation (rTMS) is widely used to modulate brain activity and treat neurological and psychiatric disorders, yet how diverse stimulation protocols shape cortical function—and whether they share common principles—remains unclear.</p> Methods <p>We combined resting-state fMRI acquired before and after single-session rTMS across nine distinct protocols targeting specific cortical regions to comprehensively map changes in the local amplitude of hemodynamic fluctuations.</p> Results <p>We found that after-effects co-varied across protocols, with similarity patterns constrained by structural and functional connectivity. Strikingly, a shared spatial pattern emerged across all protocols, closely aligned with the brain’s sensory–association hierarchy. Both shared and protocol-specific effects exhibited significant correspondence with the distribution of neurotransmitter systems. Mapping to the Neurosynth cognitive atlas revealed many-to-many correspondences between rTMS effects and cognitive domains, primarily driven by stimulation of parietal and motor regions. These rTMS-induced changes also overlapped with functional abnormalities in major depressive disorder and Parkinson’s disease, highlighting the parietal cortex as a potential transdiagnostic target. Key results were independently replicated in two datasets of multi-session rTMS.</p> Conclusions <p>These findings reveal a unified organizational framework for rTMS after-effects, grounded in cortical hierarchy, neurochemistry, and cognitive activations, offering potential guidance for neuromodulations of brain disorders.</p>