Suicidal ideation (SI) is a transdiagnostic phenomenon, co-occurring with depressive and other psychiatric disorders. Early studies support the treatment of SI in major depressive disorder with transcranial magnetic stimulation (TMS), but this application carries unique ethical issues. All causes of SI may not respond uniformly to TMS. When extrapolating from available data, clinicians must clearly communicate potential risks and benefits, informed consent, and relevant alternative treatments. Outpatient TMS specialists may hastily recommend TMS trials with omission or minimization of more suitable options to mitigate the risk of death by suicide. Furthermore, TMS clinical and research settings vary in adequacy of suicide risk assessment and its management. Since psychiatric hospitalization can preclude study participation, comparing TMS to the standard of care for actively suicidal patients poses ethical challenges. High thresholds for insurance coverage of narrow indications, as well as high out-of-pocket cost, impede equitable TMS access for those most in need within a high-risk population.