Transcranial magnetic stimulation combined with electroencephalography (TMS–EEG) allows measuring non-invasively the electrical response of the human cerebral cortex to a direct perturbation. Complementing TMS-EEG with a structural neuronavigation tool (nTMS–EEG) is key for accurately selecting cortical areas, targeting them, and adjusting the stimulation parameters based on some relevant anatomical priors. This step, together with the employment of visualization tools designed to perform a quality check of TMS-evoked potentials (TEPs) in real-time during TMS-EEG data acquisition, is pivotal for maximizing the impact of the TMS pulse on the cortex and in ensuring highly reproducible measurements within sessions and across subjects. Moreover, storing stimulation parameters in the neuronavigation system can help in replicating the stimulation parameters within and across experimental sessions and sharing them across research centers. Finally, the systematic employment of neuronavigation in TMS–EEG studies is also critical to standardize measurements in clinical populations in search for reliable diagnostic and prognostic TMS–EEG-based biomarkers for neurological and psychiatric disorders.