rTMS is an emerging intervention for medication-resistant major depression. Though effective in many cases, remission rates could bear further improvement. Improving the success rates for rTMS may require an individualized, neuroanatomically-grounded approach to diagnosis and formulation. This new approach recognizes the heterogeneity of symptoms among patients with major depression, and maps this heterogeneity on to specific domains of pathology, each associated with a specific network of regions that may serve as targets for therapeutic rTMS. Networks/domains of interest include the salience network and its role in cognitive control, the ventromedial ‘reward’ network and its role in incentive salience, and a lateral orbitofrontal network and its role in ‘non-reward’ processing. A clinical phenotype is associated with pathology in each of these networks, and the associated symptoms appear to respond well to targeted stimulation of the core nodes of each network via rTMS. Importantly, these domains of illness appear to be transdiagnostic, and may be useful for diagnostic formulation and treatment planning not only in depression but also in other presentations of psychiatric illness. Individualized treatment protocols may therefore be helpful in improving both the remission rates for rTMS in depression and also the range of illnesses for which rTMS treatment may be useful where conventional treatments fail.